1
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Graham OJ, Adamczyk EM, Schenk S, Dawkins P, Burke S, Chei E, Cisz K, Dayal S, Elstner J, Hausner ALP, Hughes T, Manglani O, McDonald M, Mikles C, Poslednik A, Vinton A, Wegener Parfrey L, Harvell CD. Manipulation of the seagrass-associated microbiome reduces disease severity. Environ Microbiol 2024; 26:e16582. [PMID: 38195072 DOI: 10.1111/1462-2920.16582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.
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Affiliation(s)
- Olivia J Graham
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily M Adamczyk
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siobhan Schenk
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phoebe Dawkins
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Samantha Burke
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Emily Chei
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kaitlyn Cisz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Sukanya Dayal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Jack Elstner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Taylor Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Omisha Manglani
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Miles McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Chloe Mikles
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Anna Poslednik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Audrey Vinton
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Laura Wegener Parfrey
- Department of Zoology and Biodiversity Research Centre, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Drew Harvell
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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2
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Mazel F, Guisan A, Parfrey LW. Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes. Mol Ecol 2024; 33:e16862. [PMID: 36786039 DOI: 10.1111/mec.16862] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/15/2023]
Abstract
Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.
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Affiliation(s)
- Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Vonaesch P, Billy V, Mann AE, Morien E, Habib A, Collard JM, Dédé M, Kapel N, Sansonetti PJ, Parfrey LW. The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status. Microlife 2023; 4:uqad033. [PMID: 37680753 PMCID: PMC10481997 DOI: 10.1093/femsml/uqad033] [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: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023]
Abstract
Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.
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Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Vincent Billy
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Allison E Mann
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Evan Morien
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Azimdine Habib
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Michel Dédé
- Laboratoire d’Analyse médicale, Institut Pasteur de Bangui, Avenue De Independence Bangui, 923 Central African Republic
| | - Nathalie Kapel
- Laboratoire de Coprologie Fonctionnelle, Assistance Publique- Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, 47-83 Bd de l’Hôpital, 75013 Paris, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Laura Wegener Parfrey
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
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Davis KM, Zeinert L, Byrne A, Davis J, Roemer C, Wright M, Parfrey LW. Successional dynamics of the cultivated kelp microbiome. J Phycol 2023; 59:538-551. [PMID: 37005360 DOI: 10.1111/jpy.13329] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 01/29/2023] [Accepted: 02/26/2023] [Indexed: 06/15/2023]
Abstract
Kelp are important primary producers that are colonized by diverse microbes that can have both positive and negative effects on their hosts. The kelp microbiome could support the burgeoning kelp cultivation sector by improving host growth, stress tolerance, and resistance to disease. Fundamental questions about the cultivated kelp microbiome still need to be addressed before microbiome-based approaches can be developed. A critical knowledge gap is how cultivated kelp microbiomes change as hosts grow, particularly following outplanting to sites that vary in abiotic conditions and microbial source pools. In this study we assessed if microbes that colonize kelp in the nursery stage persist after outplanting. We characterized microbiome succession over time on two species of kelp, Alaria marginata and Saccharina latissima, outplanted to open ocean cultivation sites in multiple geographic locations. We tested for host-species specificity of the microbiome and the effect of different abiotic conditions and microbial source pools on kelp microbiome stability during the cultivation process. We found the microbiome of kelp in the nursery is distinct from that of outplanted kelp. Few bacteria persisted on kelp following outplanting. Instead, we identified significant microbiome differences correlated with host species and microbial source pools at each cultivation site. Microbiome variation related to sampling month also indicates that seasonality in host and/or abiotic factors may influence temporal succession and microbiome turnover in cultivated kelps. This study provides a baseline understanding of microbiome dynamics during kelp cultivation and highlights research needs for applying microbiome manipulation to kelp cultivation.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Center and Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Logan Zeinert
- Centre for Applied Research, Technology and Innovation, North Island College, 1685 S Dogwood St, Campbell River, British Columbia, V9W 8C1, Canada
| | - Allison Byrne
- Centre for Applied Research, Technology and Innovation, North Island College, 1685 S Dogwood St, Campbell River, British Columbia, V9W 8C1, Canada
| | - Jonathan Davis
- School of Aquatic & Fishery Sciences, College of the Environment, University of Washington, 1122 NE Boat St, Box 355020, Seattle, Washington, 98195-5020, USA
| | - Cosmo Roemer
- M. C. Wright and Associates Ltd., 2231 Neil Drive, Nanaimo, British Columbia, V9R 6T5, Canada
| | - Michael Wright
- M. C. Wright and Associates Ltd., 2231 Neil Drive, Nanaimo, British Columbia, V9R 6T5, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Center, Department of Botany, and Department of Zoology University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
- Hakai Institute, PO Box 25039, Campbell River, British Columbia, V9W 0B7, Canada
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5
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Loudon AH, Park J, Parfrey LW. Identifying the core microbiome of the sea star Pisaster ochraceus in the context of sea star wasting disease. FEMS Microbiol Ecol 2023; 99:6998556. [PMID: 36690340 DOI: 10.1093/femsec/fiad005] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 01/21/2023] [Indexed: 01/25/2023] Open
Abstract
Sea stars are keystone species and their mass die-offs due to sea star wasting disease (SSWD) impact marine communities and have fueled recent interest in the microbiome of sea stars. We assessed the host specificity of the microbiome associated with three body regions of the sea star Pisaster ochraceus using 16S rRNA gene amplicon surveys of the bacterial communities living on and in Pisaster, their environment, and sympatric marine hosts across three populations in British Columbia, Canada. Overall, the bacterial communities on Pisaster are distinct from their environment and differ by both body region and geography. We identified core bacteria specifically associated with Pisaster across populations and nearly absent in other hosts and the environment. We then investigated the distribution of these core bacteria on SSWD-affected Pisaster from one BC site and by reanalyzing a study of SSWD on Pisaster from California. We find no differences in the distribution of core bacteria in early disease at either site and two core taxa differ in relative abundance in advanced disease in California. Using phylogenetic analyses, we find that most core bacteria have close relatives on other sea stars and marine animals, suggesting these clades have evolutionary adaptions to an animal-associated lifestyle.
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Affiliation(s)
- Andrew H Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jungsoo Park
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Hakai Institute, PO Box 25039, Campbell River, BC V9W 0B7, Canada
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Park J, Davis K, Lajoie G, Parfrey LW. Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity. Environ Microbiome 2022; 17:55. [PMID: 36384808 PMCID: PMC9670562 DOI: 10.1186/s40793-022-00451-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites. RESULTS We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus. CONCLUSIONS Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.
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Affiliation(s)
- Jungsoo Park
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Katherine Davis
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Geneviève Lajoie
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC Canada
| | - Laura Wegener Parfrey
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Department of Zoology, University of British Columbia, Vancouver, BC Canada
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Adamczyk EM, O’Connor MI, Wegener Parfrey L. Seagrass (
Zostera marina
) transplant experiment reveals core microbiome and resistance to environmental change. Mol Ecol 2022; 31:5107-5123. [DOI: 10.1111/mec.16641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 07/20/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Emily M. Adamczyk
- Department of Zoology and Biodiversity Research Centre University of British Columbia, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, 4200 ‐ 600 University Blvd Vancouver British Columbia Canada
| | - Mary I. O’Connor
- Department of Zoology and Biodiversity Research Centre University of British Columbia, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, 4200 ‐ 600 University Blvd Vancouver British Columbia Canada
| | - Laura Wegener Parfrey
- Department of Zoology and Biodiversity Research Centre University of British Columbia, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, 4200 ‐ 600 University Blvd Vancouver British Columbia Canada
- Department of Botany and Biodiversity Research Centre University of British Columbia, Unceded xʷməθkʷəy̓əm (Musqueam) Territory, 3156 ‐ 6270 University Blvd Vancouver British Columbia Canada
- Hakai Institute, PO Box 25039 Campbell River British Columbia
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8
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Lajoie G, Parfrey LW. Beyond specialization: re-examining routes of host influence on symbiont evolution. Trends Ecol Evol 2022; 37:590-598. [PMID: 35466020 DOI: 10.1016/j.tree.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 11/17/2022]
Abstract
Our understanding of host influence on microbial evolution has focused on symbiont specialization and the genomic streamlining that often accompanies it. However, a vast diversity of symbiotic lineages facultatively interact with hosts or associate with multiple hosts. Yet, there are no clear expectations for how host association influences the niche of these symbionts or their evolution. Here, we discuss how weak or variable selection on microbial symbiotic associations, horizontal transmission, and low costs of adaptation to novel host habitats are predicted to promote the expansion or maintenance of microbial niches. This broad perspective will aid in developing better and more general predictions for evolution in microbial symbioses.
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Affiliation(s)
- Geneviève Lajoie
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4.
| | - Laura Wegener Parfrey
- Botany Department, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T 1Z4
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Bodnar TS, Lee C, Wong A, Rubin I, Parfrey LW, Weinberg J. Evidence for long-lasting alterations in the fecal microbiota following prenatal alcohol exposure. Alcohol Clin Exp Res 2022; 46:542-555. [PMID: 35102585 PMCID: PMC9238389 DOI: 10.1111/acer.14784] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND There is growing evidence that the gut microbiota can be shaped by early-life experiences/exposures, with long-term consequences for brain, behavior, and health. Changes in the gut microbiota have also been identified in neurodevelopmental disorders including Autism Spectrum Disorder and schizophrenia. In contrast, no studies to date have investigated whether the gut microbiota is altered in individuals with Fetal Alcohol Spectrum Disorder (FASD), the neurodevelopmental disorder that results from prenatal alcohol exposure (PAE). The current study was designed to assess the impact of PAE on the fecal microbiota. METHODS We used a rodent model in which pregnant Sprague-Dawley rats were provided with an EtOH-containing diet or a control diet throughout gestation. Fecal samples were collected from adult male and female animals and 16s rRNA sequencing was performed. RESULTS Overall, PAE rats showed greater richness of bacterial species, with community structure investigations demonstrating distinct clustering by prenatal treatment. In addition, prenatal treatment and sex-specific alterations were observed for many specific microbes. For example, in males, Bacteroides and Bifidobacterium, and in females, Faecalitalea and Proteus, differed in abundance between PAE and control rats. CONCLUSIONS Taken together, these results show for the first time that PAE has a long-lasting and sex-specific impact on the fecal microbiota. Further research is needed that considers fetal microbiota in the development of new interventions in FASD.
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Affiliation(s)
- Tamara S. Bodnar
- Department of Cellular and Physiological Sciences, 2350 Health Sciences Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| | - Christopher Lee
- Department of Microbiology and Immunology, 2185 E Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Athena Wong
- Department of Biology, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Ilan Rubin
- Department of Zoology, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Laura Wegener Parfrey
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 109 – 2212 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Joanne Weinberg
- Department of Cellular and Physiological Sciences, 2350 Health Sciences Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
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Srivastava DS, Coristine L, Angert AL, Bontrager M, Amundrud SL, Williams JL, Yeung ACY, Zwaan DR, Thompson PL, Aitken SN, Sunday JM, O'Connor MI, Whitton J, Brown NEM, MacLeod CD, Parfrey LW, Bernhardt JR, Carrillo J, Harley CDG, Martone PT, Freeman BG, Tseng M, Donner SD. Wildcards in climate change biology. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Lemay MA, Davis KM, Martone PT, Parfrey LW. Kelp-associated Microbiota are Structured by Host Anatomy 1. J Phycol 2021; 57:1119-1130. [PMID: 33749821 DOI: 10.1111/jpy.13169] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 05/25/2023]
Abstract
Seaweed-associated microbiota are essential for the health and resilience of nearshore ecosystems, marine biogeochemical cycling, and host health. Yet much remains unknown about the ecology of seaweed-microbe symbioses. In this study, we quantified fine-scale patterns of microbial community structure across distinct anatomical regions of the kelp Laminaria setchellii. These anatomical regions represent a gradient of tissue ages: perennial holdfasts can be several years old, whereas stipe epicortex and blades are younger annual structures. Within blades, new growth occurs at the base, while the blade tips may be several months old and undergoing senescence. We hypothesized that microbial communities will differ across anatomical regions (holdfast, stipe, blade base, and blade tip), such that younger tissues will harbor fewer microbes that are more consistent across replicate individuals. Our data support this hypothesis, with the composition of bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities showing significant differences across the four anatomical regions, with the surfaces of older tissues (holdfast and blade tips) harboring significantly greater microbial richness compared to the younger tissues of the meristematic region. Additional samples collected from the surfaces of new L. setchellii recruits (<1y old) also showed differences in microbial community structure across anatomical regions, which demonstrates that these microbial differences are established early. We also observed this pattern in two additional algal species, suggesting that microbial community structure across host anatomy may be a common feature of the seaweed microbiome.
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Affiliation(s)
- Matthew A Lemay
- Hakai Institute, PO Box 309, Heriot Bay, British Columbia, V0P 1H0, Canada
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
| | - Katherine M Davis
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
| | - Patrick T Martone
- Hakai Institute, PO Box 309, Heriot Bay, British Columbia, V0P 1H0, Canada
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Hakai Institute, PO Box 309, Heriot Bay, British Columbia, V0P 1H0, Canada
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd., Vancouver, British Columbia, V6T 1Z4, Canada
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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13
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Billy V, Lhotská Z, Jirků M, Kadlecová O, Frgelecová L, Parfrey LW, Pomajbíková KJ. Blastocystis Colonization Alters the Gut Microbiome and, in Some Cases, Promotes Faster Recovery From Induced Colitis. Front Microbiol 2021; 12:641483. [PMID: 33897648 PMCID: PMC8058373 DOI: 10.3389/fmicb.2021.641483] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 12/14/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Protists are a normal component of mammalian intestinal ecosystems that live alongside, and interact with, bacterial microbiota. Blastocystis, one of the most common intestinal eukaryotes, is reported as a pathogen that causes inflammation and disease, though health consequences likely vary depending on host health, the gut ecosystem, and genetic diversity. Accumulating evidence suggests that Blastocystis is by and large commensal. Blastocystis is more common in healthy individuals than those with immune mediated diseases such as Inflammatory Bowel Diseases (IBD). Blastocystis presence is also associated with altered composition and higher richness of the bacterial gut microbiota. It is not clear whether Blastocystis directly promotes a healthy gut and microbiome or is more likely to colonize and persist in a healthy gut environment. We test this hypothesis by measuring the effect of Blastocystis ST3 colonization on the health and microbiota in a rat experimental model of intestinal inflammation using the haptenizing agent dinitrobenzene sulfonic acid (DNBS). We experimentally colonized rats with Blastocystis ST3 obtained from a healthy, asymptomatic human donor and then induced colitis after 3 weeks (short term exposure experiment) or after 13 weeks (long term exposure experiment) and compared these colonized rats to a colitis-only control group. Across experiments Blastocystis ST3 colonization alters microbiome composition, but not richness, and induces only mild gut inflammation but no clinical symptoms. Our results showed no effect of short-term exposure to Blastocystis ST3 on gut inflammation following colitis induction. In contrast, long-term Blastocystis exposure appears to promote a faster recovery from colitis. There was a significant reduction in inflammatory markers, pathology 2 days after colitis induction in the colonized group, and clinical scores also improved in this group. Blastocystis colonization resulted in a significant reduction in tumor necrosis factor alpha (TNFα) and IL-1β relative gene expression, while expression of IFNγ and IL17re/17C were elevated. We obtained similar results in a previous pilot study. We further found that bacterial richness rebounded in rats colonized by Blastocystis ST3. These results suggest that Blastocystis sp. may alter the gut ecosystem in a protective manner and promote faster recovery from disturbance.
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Affiliation(s)
- Vincent Billy
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zuzana Lhotská
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia.,Department of Medical Biology, Faculty of Science, University of South-Bohemia, České Budějovice, Czechia
| | - Milan Jirků
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Oldřiška Kadlecová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Lucia Frgelecová
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Laura Wegener Parfrey
- Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Kateřina Jirků Pomajbíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia.,Department of Medical Biology, Faculty of Science, University of South-Bohemia, České Budějovice, Czechia
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14
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Sanders-Smith R, Segovia BT, Forbes C, Hessing-Lewis M, Morien E, Lemay MA, O'Connor MI, Parfrey LW. Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.605304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.
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15
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Trevizan Segovia B, Sanders-Smith R, Adamczyk EM, Forbes C, Hessing-Lewis M, O'Connor MI, Parfrey LW. Microeukaryotic Communities Associated With the Seagrass Zostera marina Are Spatially Structured. J Eukaryot Microbiol 2020; 68:e12827. [PMID: 33065761 DOI: 10.1111/jeu.12827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 11/29/2022]
Abstract
Epibiotic microorganisms link seagrass productivity to higher trophic levels, but little is known about the processes structuring these communities, and which taxa consistently associate with seagrass. We investigated epibiotic microeukaryotes on seagrass (Zostera marina) leaves, substrates, and planktonic microeukaryotes in ten meadows in the Northeast Pacific. Seagrass epibiotic communities are distinct from planktonic and substrate communities. We found sixteen core microeukaryotes, including dinoflagellates, diatoms, and saprotrophic stramenopiles. Some likely use seagrass leaves as a substrate, others for grazing, or they may be saprotrophic organisms involved in seagrass decomposition or parasites; their relatives have been previously reported from marine sediments and in association with other hosts such as seaweeds. Core microeukaryotes were spatially structured, and none were ubiquitous across meadows. Seagrass epibiota were more spatially structured than planktonic communities, mostly due to spatial distance and changes in abiotic conditions across space. Seawater communities were relatively more similar in composition across sites and more influenced by the environmental component, but more variable over time. Core and transient taxa were both mostly structured by spatial distance and the abiotic environment, with little effect of host attributes, further indicating that those core taxa would not show a strong specific association with Z. marina.
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Affiliation(s)
- Bianca Trevizan Segovia
- Botany and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Hakai Institute, PO BOX 309, Heriot Bay, BC, V0P 1H0, Canada
| | - Rhea Sanders-Smith
- Botany and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Hakai Institute, PO BOX 309, Heriot Bay, BC, V0P 1H0, Canada
| | - Emily M Adamczyk
- Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Coreen Forbes
- Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | | | - Mary I O'Connor
- Hakai Institute, PO BOX 309, Heriot Bay, BC, V0P 1H0, Canada.,Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Botany and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada.,Hakai Institute, PO BOX 309, Heriot Bay, BC, V0P 1H0, Canada.,Zoology and Biodiversity Research Centre, University of British Columbia, Unceded xʷməθkʷəýəm (Musqueam) Territory, 3529-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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16
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Louca S, Rubin IN, Madilao LL, Bohlmann J, Doebeli M, Wegener Parfrey L. Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms. Environ Microbiol Rep 2020; 12:514-524. [PMID: 32618124 DOI: 10.1111/1758-2229.12866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ilan N Rubin
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Lufiani L Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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17
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Loudon AH, Kurtz A, Esposito E, Umile TP, Minbiole KPC, Parfrey LW, Sheafor BA. Columbia spotted frogs (Rana luteiventris) have characteristic skin microbiota that may be shaped by cutaneous skin peptides and the environment. FEMS Microbiol Ecol 2020; 96:5894915. [DOI: 10.1093/femsec/fiaa168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023] Open
Abstract
ABSTRACT
Global amphibian declines due to the fungal pathogen Batrachochytrium dendrobatidis (Bd) have led to questions about how amphibians defend themselves against skin diseases. A total of two amphibian defense mechanisms are antimicrobial peptides (AMPs), a component of amphibian innate immune defense and symbiotic skin bacteria, which can act in synergy. We characterized components of these factors in four populations of Columbia spotted frogs (Rana luteiventris) to investigate their role in disease defense. We surveyed the ability of their AMPs to inhibit Bd, skin bacterial community composition, skin metabolite profiles and presence and intensity of Bd infection. We found that AMPs from R. luteiventris inhibited Bd in bioassays, but inhibition did not correlate with Bd intensity on frogs. R. luteiventris had two prevalent and abundant core bacteria: Rhizobacter and Chryseobacterium. Rhizobacter relative abundance was negatively correlated with AMP's ability to inhibit Bd, but was not associated with Bd status itself. There was no relationship between metabolites and Bd. Bacterial communities and Bd differ by location, which suggests a strong environmental influence. R. luteiventris are dominated by consistent core bacteria, but also house transient bacteria that are site specific. Our emergent hypothesis is that host control and environmental factors shape the microbiota on R. luteiventris.
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Affiliation(s)
- A H Loudon
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - A Kurtz
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - E Esposito
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - T P Umile
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - K P C Minbiole
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - L W Parfrey
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - B A Sheafor
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
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18
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Abstract
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs. A massive survey of Earth's Bacteria and Archaea reveals that their diversity is orders of magnitude lower than previously thought. The study also indicates that extinctions played an important role in prokaryotic evolution. The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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19
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del Campo J, Kolisko M, Boscaro V, Santoferrara LF, Nenarokov S, Massana R, Guillou L, Simpson A, Berney C, de Vargas C, Brown MW, Keeling PJ, Wegener Parfrey L. EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLoS Biol 2018; 16:e2005849. [PMID: 30222734 PMCID: PMC6160240 DOI: 10.1371/journal.pbio.2005849] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/27/2018] [Indexed: 01/03/2023] Open
Abstract
Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, the European Nucleotide Archive [ENA], or the DNA DataBank of Japan [DDBJ]), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases.
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Affiliation(s)
- Javier del Campo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar—CSIC, Barcelona, Catalonia, Spain
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| | - Martin Kolisko
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Vittorio Boscaro
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luciana F. Santoferrara
- Departments of Marine Sciences & Ecology and Evolutionary Biology, University of Connecticut, Storrs, United States of America
| | - Serafim Nenarokov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar—CSIC, Barcelona, Catalonia, Spain
| | - Laure Guillou
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France
| | - Alastair Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Cedric Berney
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France
| | - Matthew W. Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Patrick J. Keeling
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura Wegener Parfrey
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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20
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Mazel F, Davis KM, Loudon A, Kwong WK, Groussin M, Parfrey LW. Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life? mSystems 2018; 3:e00097-18. [PMID: 30417109 PMCID: PMC6208643 DOI: 10.1128/msystems.00097-18] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022] Open
Abstract
Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.
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Affiliation(s)
- Florent Mazel
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katherine M. Davis
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Loudon
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K. Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Groussin
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Lemay MA, Martone PT, Hind KR, Lindstrom SC, Wegener Parfrey L. Alternate life history phases of a common seaweed have distinct microbial surface communities. Mol Ecol 2018; 27:3555-3568. [PMID: 30055017 DOI: 10.1111/mec.14815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/26/2022]
Abstract
Macroalgal life histories are complex, often involving the alternation of distinct free-living life history phases that differ in morphology, longevity and ploidy. The surfaces of marine macroalgae support diverse microbial biofilms, yet the degree of microbial variation between alternate phases is unknown. We quantified bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities on the surface of the common intertidal seaweed, Mastocarpus spp., which alternates between gametophyte (foliose, haploid) and sporophyte (encrusting, diploid) life history phases. A large portion (97%) of bacterial taxa on the surface Mastocarpus was also present in samples from the environment, indicating that macroalgal surface communities are largely assembled from the surrounding seawater. Still, changes in the relative abundance of bacterial taxa result in significantly different communities on alternate Mastocarpus life history phases, rocky substrate and seawater at all intertidal elevations. For microeukaryote assemblages, only high intertidal samples had significant differences between life history phases although sporophytes were not different from the rocky substrate at this elevation; gametophytes and sporophytes did not differ in microeukaryote communities in the mid and low zones. By sequencing three host genes, we identified three cryptic species of Mastocarpus in our data set, which co-occur in the mid-to-low intertidal zone. In these samples, M. alaskensis sporophytes harboured distinct bacterial communities compared to M. agardhii and M. intermedius sporophytes, which were not distinguishable. Conversely, microeukaryote communities did not differ among species.
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Affiliation(s)
- Matthew A Lemay
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Patrick T Martone
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Katharine R Hind
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Sandra C Lindstrom
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Laura Wegener Parfrey
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Heriot Bay, British Columbia, Canada.,Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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22
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Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M. Bacterial diversification through geological time. Nat Ecol Evol 2018; 2:1458-1467. [DOI: 10.1038/s41559-018-0625-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022]
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23
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Růžková J, Květoňová D, Jirků M, Lhotská Z, Stensvold CR, Parfrey LW, Jirků Pomajbíková K. Evaluating rodent experimental models for studies of Blastocystis ST1. Exp Parasitol 2018; 191:55-61. [PMID: 29959915 DOI: 10.1016/j.exppara.2018.06.009] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/18/2018] [Accepted: 06/26/2018] [Indexed: 01/30/2023]
Abstract
Blastocystis is a common inhabitant of the human gut, colonizing at least one billion people at a prevalence ranging from <10% to 100% in healthy human populations globally. The majority of carriers remain asymptomatic, suggesting that Blastocystis is largely a commensal, though Blastocystis has also been implicated in disease in some people. However, there are no in vivo model systems in which to experimentally test the impact of Blastocystis on mammalian hosts and the gut ecosystem and determine which factors underlie these variable clinical outcomes. We evaluated a rat model for sustaining of a human-derived Blastocystis ST1 and assess colonization success and longevity. Because of the broad host range of Blastocystis, we compared the rat with three other rodent species to establish the reproducibility of our method. Blastocystis was introduced by esophageal gavage and colonization success evaluated by Blastocystis culture. Culture was also used to determine that all animals were negative prior to colonization and negative controls remain Blastocystis-free. In this study, Blastocystis ST1 established in 100% of the outbred rats (Rattus norvegicus) and gerbils (Meriones unguiculatus) challenged. Rats were colonized asymptomatically for more than one year, but Blastocystis ST1 was not transmitted between rats. Mus musculus strain CD1 and Mastomys coucha were not susceptible to Blastocystis ST1. Thus, rats appear to be a suitable in vivo model for studies of Blastocystis ST1, as do gerbils though testing was less extensive. This work lays the foundation for experimental work on the role of Blastocystis in health and disease.
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Affiliation(s)
- Jiřina Růžková
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Branišovská 31, 370 05, Czech Republic.
| | - Dana Květoňová
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Branišovská 31, 370 05, Czech Republic.
| | - Milan Jirků
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Branišovská 31, 370 05, Czech Republic.
| | - Zuzana Lhotská
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Branišovská 31, 370 05, Czech Republic.
| | | | - Laura Wegener Parfrey
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada; Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Kateřina Jirků Pomajbíková
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Branišovská 31, 370 05, Czech Republic; Department of Medical Biology, Faculty of Science, University of South-Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic.
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24
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Parfrey LW, Moreau CS, Russell JA. Introduction: The host-associated microbiome: Pattern, process and function. Mol Ecol 2018; 27:1749-1765. [DOI: 10.1111/mec.14706] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Laura Wegener Parfrey
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada
- Department of Zoology; University of British Columbia; Vancouver British Columbia Canada
| | - Corrie S. Moreau
- Department of Science and Education; Field Museum of Natural History; Chicago IL USA
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Chen MY, Parfrey LW. Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae. Mol Ecol 2018; 27:1966-1979. [PMID: 29524281 DOI: 10.1111/mec.14548] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 11/29/2022]
Abstract
Macroalgae variably promote and deter microbial growth through release of organic carbon and antimicrobial compounds into the water column. Consequently, macroalgae influence the microbial composition of the surrounding water column and biofilms on nearby surfaces. Here, we use manipulative experiments to test the hypotheses that (i) Nereocystis luetkeana and Mastocarpus sp. macroalgae alter the water column microbiota in species-specific manner, that (ii) neighbouring macroalgae alter the bacterial communities on the surface (epibiota) of actively growing Nereocystis luetkeana meristem fragments (NMFs), and that (iii) neighbours alter NMF growth rate. We also assess the impact of laboratory incubation on macroalgal epibiota by comparing each species to wild counterparts. We find strong differences between the Nereocystis and Mastocarpus epibiota that are maintained in the laboratory. Nereocystis and Mastocarpus alter water column bacterial community composition and richness in a species specific manner, but cause only small compositional shifts on NMF surfaces that do not differ by species, and do not change richness. Co-incubation with macroalgae results in significant change in abundance of fivefold more genera in the water column compared to NMF surfaces, although the direction (i.e., enrichment or reduction) of shift is generally consistent between the water and NMF surfaces. Finally, NMFs grew during the experiment, but growth did not depend on the presence or identity of neighbouring macroalgae. Thus, macroalgae exhibit a strong and species-specific influence on the water column microbiota, but a much weaker influence on the epibiota of neighbouring macroalgae. Overall, these results support the idea that macroalgae surfaces are highly selective and demonstrate that modulations of macroalgal microbiota operate within an overarching paradigm of host species specificity.
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Affiliation(s)
- Melissa Y Chen
- Botany Department and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Botany and Zoology Departments and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Hakai Institute, Hariot Bay, BC, Canada
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26
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Louca S, Doebeli M, Parfrey LW. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome 2018; 6:41. [PMID: 29482646 PMCID: PMC5828423 DOI: 10.1186/s40168-018-0420-9] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/30/2018] [Indexed: 05/13/2023]
Abstract
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R2<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.
- Department of Zoology, University of British Columbia, Vancouver, Canada.
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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Lemay MA, Martone PT, Keeling PJ, Burt JM, Krumhansl KA, Sanders RD, Wegener Parfrey L. Sympatric kelp species share a large portion of their surface bacterial communities. Environ Microbiol 2018; 20:658-670. [PMID: 29124859 DOI: 10.1111/1462-2920.13993] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 12/13/2022]
Abstract
Kelp forest ecosystems are biodiversity hotspots, providing habitat for dense assemblages of marine organisms and nutrients for marine and terrestrial food webs. The surfaces of kelps support diverse microbial communities that facilitate the transfer of carbon from algal primary production to higher trophic levels. We quantified the diversity of bacteria on the surfaces of eight sympatric kelp species from four sites in British Columbia. Kelp-associated bacterial communities are significantly different from their environment, even though 86% of their bacterial taxa are shared with seawater and 97% are shared with rocky substrate. This differentiation is driven by differences in relative abundance of the bacterial taxa present. Similarly, a large portion of bacterial taxa (37%) is shared among all eight kelp species, yet differential abundance of bacterial taxa underlies differences in community structure among species. Kelp-associated bacterial diversity does not track host phylogeny; instead bacterial community composition is correlated with the life-history strategy of the host, with annual and perennial kelps supporting divergent bacterial communities. These data provide the first community-scale investigation of kelp forest-associated bacterial diversity. More broadly, this study provides insight into mechanisms that may structure bacterial communities among closely related sympatric host species.
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Affiliation(s)
- Matthew A Lemay
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
| | - Patrick T Martone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
| | - Patrick J Keeling
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
| | - Jenn M Burt
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
- School of Resource and Environmental Management, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6
| | - Kira A Krumhansl
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
- School of Resource and Environmental Management, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6
| | - Rhea D Sanders
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
| | - Laura Wegener Parfrey
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
- Hakai Institute, PO Box 309, Heriot Bay, BC, Canada V0P 1H0
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
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Arrieta MC, Arévalo A, Stiemsma L, Dimitriu P, Chico ME, Loor S, Vaca M, Boutin RCT, Morien E, Jin M, Turvey SE, Walter J, Parfrey LW, Cooper PJ, Finlay B. Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting. J Allergy Clin Immunol 2017; 142:424-434.e10. [PMID: 29241587 PMCID: PMC6075469 DOI: 10.1016/j.jaci.2017.08.041] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [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: 03/30/2017] [Revised: 07/27/2017] [Accepted: 08/23/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment. OBJECTIVE We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting. METHODS We conducted a case-control study nested within a birth cohort from rural Ecuador in which we identified 27 children with atopic wheeze and 70 healthy control subjects at 5 years of age. We analyzed bacterial and eukaryotic gut microbiota in stool samples collected at 3 months of age using 16S and 18S sequencing. Bacterial metagenomes were predicted from 16S rRNA data by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and categorized by function with Kyoto Encyclopedia of Genes and Genomes ontology. Concentrations of fecal short-chain fatty acids were determined by using gas chromatography. RESULTS As previously observed in Canadian infants, microbial dysbiosis at 3 months of age was associated with later development of atopic wheeze. However, the dysbiosis in Ecuadorian babies involved different bacterial taxa, was more pronounced, and also involved several fungal taxa. Predicted metagenomic analysis emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. Levels of the fecal short-chain fatty acids acetate and caproate were reduced and increased, respectively, in the 3-month stool samples of children who went on to have atopic wheeze. CONCLUSIONS Our findings support the importance of fungal and bacterial microbiota during the first 100 days of life on the development of atopic wheeze and provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy.
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Affiliation(s)
- Marie-Claire Arrieta
- Michael Smith Laboratories and the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Andrea Arévalo
- Facultad de Ciencias Medicas, de la Salud y la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Leah Stiemsma
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, Calif
| | - Pedro Dimitriu
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martha E Chico
- Fundación Ecuatoriana Para Investigación en Salud, Quito, Ecuador
| | - Sofia Loor
- Fundación Ecuatoriana Para Investigación en Salud, Quito, Ecuador
| | - Maritza Vaca
- Fundación Ecuatoriana Para Investigación en Salud, Quito, Ecuador
| | - Rozlyn C T Boutin
- Michael Smith Laboratories and the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Morien
- Departments of Zoology and Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mingliang Jin
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Laura Wegener Parfrey
- Departments of Zoology and Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Philip J Cooper
- Facultad de Ciencias Medicas, de la Salud y la Vida, Universidad Internacional del Ecuador, Quito, Ecuador; Fundación Ecuatoriana Para Investigación en Salud, Quito, Ecuador; Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - Brett Finlay
- Michael Smith Laboratories and the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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29
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Wegener Parfrey L, Jirků M, Šíma R, Jalovecká M, Sak B, Grigore K, Jirků Pomajbíková K. A benign helminth alters the host immune system and the gut microbiota in a rat model system. PLoS One 2017; 12:e0182205. [PMID: 28771620 PMCID: PMC5542714 DOI: 10.1371/journal.pone.0182205] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 07/16/2017] [Indexed: 12/26/2022] Open
Abstract
Helminths and bacteria are major players in the mammalian gut ecosystem and each influences the host immune system and health. Declines in helminth prevalence and bacterial diversity appear to play a role in the dramatic rise of immune mediated inflammatory diseases (IMIDs) in western populations. Helminths are potent modulators of immune system and their reintroduction is a promising therapeutic avenue for IMIDs. However, the introduction of helminths represents a disturbance for the host and it is important to understand the impact of helminth reintroduction on the host, including the immune system and gut microbiome. We tested the impact of a benign tapeworm, Hymenolepis diminuta, in a rat model system. We find that H. diminuta infection results in increased interleukin 10 gene expression in the beginning of the prepatent period, consistent with induction of a type 2 immune response. We also find induction of humoral immunity during the patent period, shown here by increased IgA in feces. Further, we see an immuno-modulatory effect in the small intestine and spleen in patent period, as measured by reductions in tissue immune cells. We observed shifts in microbiota community composition during the patent period (beta-diversity) in response to H. diminuta infection. However, these compositional changes appear to be minor; they occur within families and genera common to both treatment groups. There was no change in alpha diversity. Hymenolepis diminuta is a promising model for helminth therapy because it establishes long-term, stable colonization in rats and modulates the immune system without causing bacterial dysbiosis. These results suggest that the goal of engineering a therapeutic helminth that can safely manipulate the mammalian immune system without disrupting the rest of the gut ecosystem is in reach.
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Affiliation(s)
- Laura Wegener Parfrey
- Departments of Botany and Zoology, University of British Columbia, Vancouver, Canada.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, Canada
| | - Milan Jirků
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Radek Šíma
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Marie Jalovecká
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Bohumil Sak
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karina Grigore
- Departments of Botany and Zoology, University of British Columbia, Vancouver, Canada
| | - Kateřina Jirků Pomajbíková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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30
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Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. UniEuk: Time to Speak a Common Language in Protistology! J Eukaryot Microbiol 2017; 64:407-411. [PMID: 28337822 PMCID: PMC5435949 DOI: 10.1111/jeu.12414] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.
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Affiliation(s)
- Cédric Berney
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - Andreea Ciuprina
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany
| | - Sara Bender
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Juliet Brodie
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA
| | - Jeena Rajan
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Laura Wegener Parfrey
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada
| | - Stéphane Audic
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA
| | - Guy Cochrane
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Lucas Czech
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Frank Oliver Glöckner
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.,Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | | | - Christian Quast
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Jonathan Z Kaye
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.,Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany
| | - Javier Del Campo
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Colomban de Vargas
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
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Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M. High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 2016; 1:15. [PMID: 28812567 DOI: 10.1038/s41559-016-0015] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 01/08/2023]
Abstract
Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Institute of Applied Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada
| | - Saulo M S Jacques
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.,Programa de Pós-Graduação em Ecologia e Evolugão, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, 20550-013, Brazil
| | - Aliny P F Pires
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Juliana S Leal
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-971, Brazil
| | - Diane S Srivastava
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Vinicius F Farjalla
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada
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Avena CV, Parfrey LW, Leff JW, Archer HM, Frick WF, Langwig KE, Kilpatrick AM, Powers KE, Foster JT, McKenzie VJ. Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment. Front Microbiol 2016; 7:1753. [PMID: 27909426 PMCID: PMC5112243 DOI: 10.3389/fmicb.2016.01753] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [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: 06/01/2016] [Accepted: 10/19/2016] [Indexed: 02/01/2023] Open
Abstract
Bats are geographically widespread and play an important role in many ecosystems, but relatively little is known about the ecology of their associated microbial communities and the role microbial taxa play in bat health, development, and evolution. Moreover, few vertebrate animal skin microbiomes have been comprehensively assessed, and thus characterizing the bat skin microbiome will yield valuable insight into the variability of vertebrate skin microbiomes as a whole. The recent emergence of the skin fungal disease white-nose syndrome highlights the potentially important role bat skin microbial communities could play in bat health. Understanding the determinant of bat skin microbial communities could provide insight into important factors allowing individuals to persist with disease. We collected skin swabs from a total of 11 bat species from the eastern United States (n = 45) and Colorado (n = 119), as well as environmental samples (n = 38) from a subset of sites, and used 16S rRNA marker gene sequencing to observe bacterial communities. In addition, we conducted a literature survey to compare the skin microbiome across vertebrate groups, including the bats presented in this study. Host species, region, and site were all significant predictors of the variability across bat skin bacterial communities. Many bacterial taxa were found both on bats and in the environment. However, some bacterial taxa had consistently greater relative abundances on bat skin relative to their environments. Bats shared many of their abundant taxa with other vertebrates, but also hosted unique bacterial lineages such as the class Thermoleophilia (Actinobacteria). A strong effect of site on the bat skin microbiome indicates that the environment very strongly influences what bacteria are present on bat skin. Bat skin microbiomes are largely composed of site-specific microbiota, but there do appear to be important host-specific taxa. How this translates to differences in host-microbial interactions and bat health remains an important knowledge gap, but this work suggests that habitat variability is very important. We identify some bacterial groups that are more consistent on bats despite site differences, and these may be important ones to study in terms of their function as potential core microbiome members.
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Affiliation(s)
- Christine V Avena
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder Boulder, CO, USA
| | - Laura Wegener Parfrey
- Departments of Botany and Zoology, University of British Columbia Vancouver, BC, Canada
| | - Jonathan W Leff
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, USA; Cooperative Institute for Research in Environmental Sciences, University of Colorado BoulderBoulder, CO, USA
| | - Holly M Archer
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder Boulder, CO, USA
| | - Winifred F Frick
- Department of Ecology and Evolutionary Biology, University of California, Santa CruzSanta Cruz, CA, USA; Bat Conservation InternationalAustin, TX, USA
| | - Kate E Langwig
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz Santa Cruz, CA, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz Santa Cruz, CA, USA
| | | | - Jeffrey T Foster
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire Durham, NH, USA
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder Boulder, CO, USA
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Loudon AH, Venkataraman A, Van Treuren W, Woodhams DC, Parfrey LW, McKenzie VJ, Knight R, Schmidt TM, Harris RN. Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin. Front Microbiol 2016; 7:333. [PMID: 27014249 PMCID: PMC4793798 DOI: 10.3389/fmicb.2016.00333] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 01/05/2016] [Accepted: 03/02/2016] [Indexed: 02/01/2023] Open
Abstract
Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection, <1% of bacteria that were consistent with random dispersal and none of the bacteria that were consistent under negative selection had a 97% or greater match to antifungal isolates. Additionally we performed an experiment where salamanders were either provided or denied a bacterial reservoir and estimated immigration and loss (emigration and local extinction) rates of bacteria on salamanders in both treatments. Loss was strongly related to bacterial richness, suggesting competition is important for structuring the community. Bacteria closely related to antifungal isolates were more likely to persist on salamanders with or without a bacterial reservoir, suggesting they had a competitive advantage. Furthermore, over-represented and under-represented operational taxonomic units (OTUs) had similar persistence on salamanders when a bacterial reservoir was present. However, under-represented OTUs were less likely to persist in the absence of a bacterial reservoir, suggesting that the over-represented and under-represented bacteria were selected against or for on salamanders through time. Our findings from the neutral model, migration and persistence analyses show that bacteria that exhibit a high similarity to antifungal isolates persist on salamanders, which likely protect hosts against pathogens and improve fitness. This research is one of the first to apply ecological theory to investigate assembly of host associated-bacterial communities, which can provide insights for probiotic bioaugmentation as a conservation strategy against disease.
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Affiliation(s)
- Andrew H Loudon
- Department of Biology, James Madison University, Harrisonburg VA, USA
| | | | | | - Douglas C Woodhams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO, USA
| | | | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO, USA
| | - Rob Knight
- BioFrontiers Institute, University of Colorado, Boulder CO, USA
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor MI, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg VA, USA
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34
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Wegener Parfrey L. Mock communities highlight the diversity of host-associated eukaryotes. Mol Ecol 2015; 24:4337-9. [PMID: 26311623 DOI: 10.1111/mec.13311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 01/15/2023]
Abstract
Host-associated microbes are ubiquitous. Every multicellular eukaryote, and even many unicellular eukaryotes (protists), hosts a diverse community of microbes. High-throughput sequencing (HTS) tools have illuminated the vast diversity of host-associated microbes and shown that they have widespread influence on host biology, ecology and evolution (McFall-Ngai et al. ). Bacteria receive most of the attention, but protists are also important components of microbial communities associated with humans (Parfrey et al. ) and other hosts. As HTS tools are increasingly used to study eukaryotes, the presence of numerous and diverse host-associated eukaryotes is emerging as a common theme across ecosystems. Indeed, HTS studies demonstrate that host-associated lineages account for between 2 and 12% of overall eukaryotic sequences detected in soil, marine and freshwater data sets, with much higher relative abundances observed in some samples (Ramirez et al. ; Simon et al. ; de Vargas et al. ). Previous studies in soil detected large numbers of predominantly parasitic lineages such as Apicomplexa, but did not delve into their origin [e.g. (Ramirez et al. )]. In this issue of Molecular Ecology, Geisen et al. () use mock communities to show that many of the eukaryotic organisms detected by environmental sequencing in soils are potentially associated with animal hosts rather than free-living. By isolating the host-associated fraction of soil microbial communities, Geisen and colleagues help explain the surprisingly high diversity of parasitic eukaryotic lineages often detected in soil/terrestrial studies using high-throughput sequencing (HTS) and reinforce the ubiquity of these host-associated microbes. It is clear that we can no longer assume that organisms detected in bulk environmental sequencing are free-living, but instead need to design studies that specifically enumerate the diversity and function of host-associated eukaryotes. Doing so will allow the field to determine the role host-associated eukaryotes play in soils and other environments and to evaluate hypotheses on assembly of host-associated communities, disease ecology and more.
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Affiliation(s)
- Laura Wegener Parfrey
- Departments of Botany and Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada, V6T1Z4.,Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, ON, Canada
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35
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Affiliation(s)
- Julius Lukeš
- Institute of Parasitology, Biology Centre, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Canadian Institute for Advanced Research, Toronto, Canada
| | | | | | - Laura Wegener Parfrey
- Canadian Institute for Advanced Research, Toronto, Canada
- Departments of Botany and Zoology, University of British Columbia, Vancouver, Canada
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36
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Korajkic A, Parfrey LW, McMinn BR, Baeza YV, VanTeuren W, Knight R, Shanks OC. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water. Water Res 2015; 69:30-39. [PMID: 25463929 DOI: 10.1016/j.watres.2014.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/08/2014] [Accepted: 11/04/2014] [Indexed: 05/12/2023]
Abstract
Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is known about how these communities change due to mixing and subsequent decomposition of the sewage contaminant. We investigated decay of sewage in upper Mississippi River using Illumina sequencing of 16S and 18S rRNA gene hypervariable regions and qPCR for human-associated and general fecal Bacteroidales indicators. Mixtures of primary treated sewage and river water were placed in dialysis bags and incubated in situ under ambient conditions for seven days. We assessed changes in microbial community composition under two treatments in a replicated factorial design: sunlight exposure versus shaded and presence versus absence of native river microbiota. Initial diversity was higher in sewage compared to river water for 16S sequences, but the reverse was observed for 18S sequences. Both treatments significantly shifted community composition for eukaryotes and bacteria (P < 0.05). Data indicated that the presence of native river microbiota, rather than exposure to sunlight, accounted for the majority of variation between treatments for both 16S (R = 0.50; P > 0.001) and 18S (R = 0.91; P = 0.001) communities. A comparison of 16S sequence data and fecal indicator qPCR measurements indicated that the latter was a good predictor of overall bacterial community change over time (rho: 0.804-0.814, P = 0.001). These findings suggest that biotic interactions, such as predation by bacterivorous protozoa, can be critical factors in the decomposition of sewage in freshwater habitats and support the use of Bacteroidales genetic markers as indicators of fecal pollution.
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Affiliation(s)
- Asja Korajkic
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, USA
| | | | - Brian R McMinn
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Cincinnati, USA
| | | | - Will VanTeuren
- Biofrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Rob Knight
- Biofrontiers Institute, University of Colorado, Boulder, CO, USA; Howard Hughes Medical Institute, Boulder, CO, USA
| | - Orin C Shanks
- National Risk Management Research Laboratory, US. Environmental Protection Agency, Cincinnati, USA.
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37
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Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol 2014; 5:298. [PMID: 24995004 PMCID: PMC4063188 DOI: 10.3389/fmicb.2014.00298] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [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: 02/26/2014] [Accepted: 05/30/2014] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.
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Affiliation(s)
| | - William A Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, CO, USA
| | - Christian L Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Jose C Clemente
- Biofrontiers Institute, University of Colorado Boulder, CO, USA
| | | | | | | | | | | | | | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago Chicago, IL, USA ; Institute of Genomic and Systems Biology, Argonne National Laboratory Argonne, IL, USA
| | - Rob Knight
- Biofrontiers Institute, University of Colorado Boulder, CO, USA ; Howard Hughes Medical Institute, University of Colorado Boulder, CO, USA
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38
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Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res 2013; 42:D643-8. [PMID: 24293649 PMCID: PMC3965112 DOI: 10.1093/nar/gkt1209] [Citation(s) in RCA: 1723] [Impact Index Per Article: 156.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.
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Affiliation(s)
- Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany, Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada, Department of Zoology, University of British Columbia, Vancouver V6T 1Z4, Canada, Ribocon GmbH, D-28359 Bremen, Germany, School of Engineering and Science, Jacobs University Bremen gGmbH, D-28759 Bremen, Germany and Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany
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39
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Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DPB, Frank DN, Li E, Horvath S, Knight R, Braun J. A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. PLoS One 2013; 8:e80702. [PMID: 24260458 PMCID: PMC3834335 DOI: 10.1371/journal.pone.0080702] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/07/2013] [Indexed: 02/08/2023] Open
Abstract
Abnormalities of the intestinal microbiota are implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC), two spectra of inflammatory bowel disease (IBD). However, the high complexity and low inter-individual overlap of intestinal microbial composition are formidable barriers to identifying microbial taxa representing this dysbiosis. These difficulties might be overcome by an ecologic analytic strategy to identify modules of interacting bacteria (rather than individual bacteria) as quantitative reproducible features of microbial composition in normal and IBD mucosa. We sequenced 16S ribosomal RNA genes from 179 endoscopic lavage samples from different intestinal regions in 64 subjects (32 controls, 16 CD and 16 UC patients in clinical remission). CD and UC patients showed a reduction in phylogenetic diversity and shifts in microbial composition, comparable to previous studies using conventional mucosal biopsies. Analysis of weighted co-occurrence network revealed 5 microbial modules. These modules were unprecedented, as they were detectable in all individuals, and their composition and abundance was recapitulated in an independent, biopsy-based mucosal dataset 2 modules were associated with healthy, CD, or UC disease states. Imputed metagenome analysis indicated that these modules displayed distinct metabolic functionality, specifically the enrichment of oxidative response and glycan metabolism pathways relevant to host-pathogen interaction in the disease-associated modules. The highly preserved microbial modules accurately classified IBD status of individual patients during disease quiescence, suggesting that microbial dysbiosis in IBD may be an underlying disorder independent of disease activity. Microbial modules thus provide an integrative view of microbial ecology relevant to IBD.
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Affiliation(s)
- Maomeng Tong
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiaoxiao Li
- Cedars-Sinai F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California, United States of America
| | - Laura Wegener Parfrey
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | - Bennett Roth
- Department of Medicine, Division of Digestive Disease, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Andrew Ippoliti
- Cedars-Sinai F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California, United States of America
| | - Bo Wei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America
| | - Dermot P. B. McGovern
- Cedars-Sinai F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California, United States of America
| | - Daniel N. Frank
- Division of Infectious Diseases, University of Colorado, School of Medicine, Aurora, Colorado, United States of America
- Union Council, Denver Microbiome Research Consortium (MiRC), University of Colorado, School of Medicine, Aurora, Colorado, United States of America
| | - Ellen Li
- Department of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Steve Horvath
- Department of Human Genetics and Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Rob Knight
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, United States of America
- Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America;
| | - Jonathan Braun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
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40
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Kueneman JG, Parfrey LW, Woodhams DC, Archer HM, Knight R, McKenzie VJ. The amphibian skin-associated microbiome across species, space and life history stages. Mol Ecol 2013; 23:1238-1250. [PMID: 24171949 DOI: 10.1111/mec.12510] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 12/18/2022]
Abstract
Skin-associated bacteria of amphibians are increasingly recognized for their role in defence against pathogens, yet we have little understanding of their basic ecology. Here, we use high-throughput 16S rRNA gene sequencing to examine the host and environmental influences on the skin microbiota of the cohabiting amphibian species Anaxyrus boreas, Pseudacris regilla, Taricha torosa and Lithobates catesbeianus from the Central Valley in California. We also studied populations of Rana cascadae over a large geographic range in the Klamath Mountain range of Northern California, and across developmental stages within a single site. Dominant bacterial phylotypes on amphibian skin included taxa from Bacteroidetes, Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Sphingobacteria and Actinobacteria. Amphibian species identity was the strongest predictor of microbial community composition. Secondarily, within a given amphibian species, wetland site explained significant variation. Amphibian-associated microbiota differed systematically from microbial assemblages in their environments. Rana cascadae tadpoles have skin bacterial communities distinct from postmetamorphic conspecifics, indicating a strong developmental shift in the skin microbes following metamorphosis. Establishing patterns observed in the skin microbiota of wild amphibians and environmental factors that underlie them is necessary to understand skin symbiont community assembly, and ultimately, the role skin microbiota play in the extended host phenotype including disease resistance.
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Affiliation(s)
- Jordan G Kueneman
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N-122, UCB 334, Boulder, CO, 80309, USA
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Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2013; 2:e01104. [PMID: 24137541 PMCID: PMC3796315 DOI: 10.7554/elife.01104] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [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: 06/19/2013] [Accepted: 09/20/2013] [Indexed: 12/13/2022] Open
Abstract
Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI:http://dx.doi.org/10.7554/eLife.01104.001 Our bodies—especially our skin, our saliva, the lining of our mouth and our gastrointestinal tract—are home to a diverse collection of bacteria and other microorganisms called the microbiome. While the roles played by many of these microorganisms have yet to be identified, it is known that they contribute to the health and wellbeing of their host by metabolizing indigestible compounds, producing essential vitamins, and preventing the growth of harmful bacteria. They are important for nutrient and carbon cycling in the environment. The advent of advanced sequencing techniques has made it feasible to study the composition of this microbial community, and to monitor how it changes over time or how it responds to events such as antibiotic treatment. Sequencing studies have been used to highlight the significant differences between microbial communities found in different parts of the body, and to follow the evolution of the gut microbiome from birth. Most of these studies have focused on live animals, so little is known about what happens to the microbiome after its host dies. In particular, it is not known if the changes that occur after death are similar for all individuals. Moreover, the decomposing animal supplies nutrients and carbon to the surrounding ecosystem, but its influence on the microbial community of its immediate environment is not well understood. Now Metcalf et al. have used high-throughput sequencing to study the bacteria and other microorganisms (such as nematodes and fungi) in dead and decomposing mice, and also in the soil beneath them, over the course of 48 days. The changes were significant and also consistent across the corpses, with the microbial communities in the corpses influencing those in the soil, and vice versa. Metcalf et al. also showed that these measurements could be used to estimate the postmortem interval (the time since death) to within approximately 3 days, which suggests that the work could have applications in forensic science. DOI:http://dx.doi.org/10.7554/eLife.01104.002
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Affiliation(s)
- Jessica L Metcalf
- Biofrontiers Institute , University of Colorado at Boulder , Boulder , United States
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Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol 2013; 23:1301-1317. [PMID: 24118574 DOI: 10.1111/mec.12501] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 12/19/2022]
Abstract
Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, neighbour-net networks and beta-diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks and aardwolves), even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.
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Affiliation(s)
- Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554-CNRS-IRD, Université Montpellier 2, Montpellier, France; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA; Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
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Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE. Meeting report: fungal its workshop (october 2012). Stand Genomic Sci 2013; 8:118-23. [PMID: 23961317 PMCID: PMC3739174 DOI: 10.4056/sigs.3737409] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report summarizes a meeting held in Boulder, CO USA (19-20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the primary goal of supporting collaboration among researchers for improving fungal ITS sequence resources and developing recommendations for standard ITS primers for the research community.
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Affiliation(s)
- Scott T Bates
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
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Parfrey LW, Lahr DJG. Multicellularity arose several times in the evolution of eukaryotes (Response to DOI 10.1002/bies.201100187). Bioessays 2013; 35:339-47. [DOI: 10.1002/bies.201200143] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Abstract
Rapidly developing sequencing methods and analytical techniques are enhancing our ability to understand the human microbiome, and, indeed, how the microbiome and its constituents are defined. This review highlights recent research that expands our ability to understand the human microbiome on different spatial and temporal scales, including daily time series datasets spanning months. Furthermore, emerging concepts related to defining operational taxonomic units, diversity indices, core versus transient microbiomes, and the possibility of enterotypes are discussed. Additional advances in sequencing technology and in our understanding of the microbiome will provide exciting prospects for exploiting the microbiota for personalized medicine.
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Affiliation(s)
- Luke K Ursell
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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46
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Abstract
The knowledge that our bodies are home to microbes is not new; van Leeuwenhoek first saw the microbes of the mouth and gut over three centuries ago. However, next generation sequencing technologies are enabling us to characterize our microbial consortia on an unprecedented scale, and are providing new insights into the range of variability of our microbiota and their contributions to our health. The microbiota far outnumber the human component of our selves, with 10 times more cells and at least 100 times more genes. Moreover, while individuals share over 99.9% of their human genome sequence, there are vast differences in the microbiome (the collection of genes of our associated microbes). This raises the question of the extent to which our microbial community determines our human physiological responses and susceptibility to disease. In order to develop technologies that allow us to manipulate the microbiome to improve health we must first understand the factors that influence spatial and temporal variation, stability in response to perturbation, and conditions that induce community-wide changes.
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Affiliation(s)
- L W Parfrey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
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47
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Abstract
The human gut harbors diverse microbes that play a fundamental role in the well-being of their host. The constituents of the microbiota--bacteria, viruses, and eukaryotes--have been shown to interact with one another and with the host immune system in ways that influence the development of disease. We review these interactions and suggest that a holistic approach to studying the microbiota that goes beyond characterization of community composition and encompasses dynamic interactions between all components of the microbiota and host tissue over time will be crucial for building predictive models for diagnosis and treatment of diseases linked to imbalances in our microbiota.
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Affiliation(s)
- Jose C Clemente
- Department of Chemistry & Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
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48
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Abstract
The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial groups "topped" by a crown-containing plants, animals, and fungi and their microbial relatives. Although more recent multigene concatenated analyses have refined the relationships among the many branches of eukaryotes, the root of the eukaryotic tree of life has remained elusive. Inferring the root of extant eukaryotes is challenging because of the age of the group (∼1.7-2.1 billion years old), tremendous heterogeneity in rates of evolution among lineages, and lack of obvious outgroups for many genes. Here, we reconstruct a rooted phylogeny of extant eukaryotes based on minimizing the number of duplications and losses among a collection of gene trees. This approach does not require outgroup sequences or assumptions of orthology among sequences. We also explore the impact of taxon and gene sampling and assess support for alternative hypotheses for the root. Using 20 gene trees from 84 diverse eukaryotic lineages, this approach recovers robust eukaryotic clades and reveals evidence for a eukaryotic root that lies between the Opisthokonta (animals, fungi and their microbial relatives) and all remaining eukaryotes.
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Affiliation(s)
- Laura A Katz
- Department of Biological Sciences, Smith College, 44 College Lane, Northampton, MA 01063, USA.
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49
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Zaneveld JRR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends Microbiol 2011; 19:472-82. [PMID: 21872475 PMCID: PMC3184378 DOI: 10.1016/j.tim.2011.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 01/21/2023]
Abstract
High-throughput sequencing technologies provide new opportunities to address longstanding questions about habitat adaptation in microbial organisms. How have microbes managed to adapt to such a wide range of environments, and what genomic features allow for such adaptation? We review recent large-scale studies of habitat adaptation, with emphasis on those that utilize phylogenetic techniques. On the basis of current trends, we summarize methodological challenges faced by investigators, and the tools, techniques and analytical approaches available to overcome them. Phylogenetic approaches and detailed information about each environmental sample will be crucial as the ability to collect genome sequences continues to expand.
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Affiliation(s)
- Jesse R R Zaneveld
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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50
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Lahr DJG, Parfrey LW, Mitchell EAD, Katz LA, Lara E. The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms. Proc Biol Sci 2011; 278:2081-90. [PMID: 21429931 PMCID: PMC3107637 DOI: 10.1098/rspb.2011.0289] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/04/2011] [Indexed: 11/12/2022] Open
Abstract
Amoebae are generally assumed to be asexual. We argue that this view is a relict of early classification schemes that lumped all amoebae together inside the 'lower' protozoa, separated from the 'higher' plants, animals and fungi. This artificial classification allowed microbial eukaryotes, including amoebae, to be dismissed as primitive, and implied that the biological rules and theories developed for macro-organisms need not apply to microbes. Eukaryotic diversity is made up of 70+ lineages, most of which are microbial. Plants, animals and fungi are nested among these microbial lineages. Thus, theories on the prevalence and maintenance of sex developed for macro-organisms should in fact apply to microbial eukaryotes, though the theories may need to be refined and generalized (e.g. to account for the variation in sexual strategies and prevalence of facultative sex in natural populations of many microbial eukaryotes). We use a revised phylogenetic framework to assess evidence for sex in several amoeboid lineages that are traditionally considered asexual, and we interpret this evidence in light of theories on the evolution of sex developed for macro-organisms. We emphasize that the limited data available for many lineages coupled with natural variation in microbial life cycles overestimate the extent of asexuality. Mapping sexuality onto the eukaryotic tree of life demonstrates that the majority of amoeboid lineages are, contrary to popular belief, anciently sexual, and that most asexual groups have probably arisen recently and independently. Additionally, several unusual genomic traits are prevalent in amoeboid lineages, including cyclic polyploidy, which may serve as alternative mechanisms to minimize the deleterious effects of asexuality.
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Affiliation(s)
- Daniel J. G. Lahr
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Laura Wegener Parfrey
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Edward A. D. Mitchell
- Laboratory of Soil Biology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Laura A. Katz
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Enrique Lara
- Laboratory of Soil Biology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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