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Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Sanders K, Schwartz A, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE, Kaddurah-Daouk R, Knight R, Bendlin BB. Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.04.24313004. [PMID: 39281749 PMCID: PMC11398448 DOI: 10.1101/2024.09.04.24313004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
BACKGROUND The gut microbiome is a potentially modifiable factor in Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited. METHODS Shallow-shotgun metagenomic data was used to analyze fecal microbiome from participants enrolled in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies. RESULTS Gut microbiome composition and function differed between people with AD and cognitively unimpaired individuals. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies. DISCUSSION These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.
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Affiliation(s)
- Jea Woo Kang
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Lora A Khatib
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
- Neurosciences Graduate Program, University of California San Diego, La Jolla, California, USA Address: 9500 Gilman Dr, La Jolla, CA, USA 92093
| | - Margo B Heston
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Amanda H Dilmore
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
| | - Jennifer S Labus
- Integrative Biostatistics and Bioinformatics Core (IBBC) at the Goodman-Luskin Microbiome Center Address: 42-210 CHS, Los Angeles, CA, USA 90095
- G. Oppenheimer Center for Neurobiology of Stress and Resilience Address: 10833 Le Conte Ave, Los Angeles, CA, USA 90095
- UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine at UCLA Address: 100 Medical Plaza, Los Angeles, CA, USA 90095
| | - Yuetiva Deming
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Leyla Schimmel
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA Address: 905 W Main St, Durham, NC, USA 27701
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA Address: 300 N Duke St, Durham, NC, USA 27701
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
| | - MacKenzie Bryant
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
| | - Ara Schwartz
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
| | - Tyler K Ulland
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA Address: 1685 Highland Ave, Madison, WI, USA 53705
| | - Sterling C Johnson
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Cynthia M Carlsson
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Nathaniel A Chin
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden Address: Blå stråket 15, vån 3 SU/Sahlgrenska 413 45 Göteborg, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden Address: Blå stråket 15, vån 3 SU/Sahlgrenska 413 45 Göteborg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden Address: Blå stråket 5, 413 45 Göteborg, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK Address: Queen Square, London WC1N 3BG, United Kingdom
- UK Dementia Research Institute at UCL, London, UK Address: 6th Floor, Maple House, Tottenham Ct Rd, London W1T 7NF, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China Address: Units 1501-1502, 1512-1518, 15/F, Building 17W, Hong Kong Science Park, Shatin, N.T., Hong Kong
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA Address: 1550 Linden Dr, Madison, WI, USA 53706
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA Address: 905 W Main St, Durham, NC, USA 27701
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA Address: 308 Research Dr, Durham, NC, USA 27710
- Department of Medicine, Duke University, Durham, NC, USA Address: 40 Duke Medicine Circle, 124 Davison Building, Durham, NC, USA 27710
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA Address: 9461 Gilman Dr, La Jolla, CA, USA 92093
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA Address: Franklin Antonio Hall, Jacobs School of Engineering, 9500 Gilman Dr, La Jolla, CA, USA 92093
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA Address: 3235 Voigt Dr, La Jolla, CA, USA 92093
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA Address: 3234 Matthews Ln, La Jolla, CA, USA 92093
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA Address: 3223 Voigt Dr, La Jolla, CA, USA 92093
| | - Barbara B Bendlin
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 600 Highland Ave, J5/1 Mezzanine, Madison, WI, USA 53792
- Wisconsin Alzheimer's Institute, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA Address: 610 Walnut Street, 9th Floor, Madison, WI, USA 53726
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Benedict C, Delgado A, Pen I, Vaga C, Daly M, Quattrini AM. Sea anemone (Anthozoa, Actiniaria) diversity in Mo'orea (French Polynesia). Mol Phylogenet Evol 2024; 198:108118. [PMID: 38849066 DOI: 10.1016/j.ympev.2024.108118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo'orea (French Polynesia) with the use of a dataset from the Mo'orea Biocode's "BioBlitz" initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo'orea's diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo'orea, spotlighting the area's ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.
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Affiliation(s)
- Charlotte Benedict
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA.
| | - Alonso Delgado
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | - Isabel Pen
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | - Claudia Vaga
- Department of Invertebrate Zoology, Smithsonian Institution's National Museum of Natural History, 10th and Constitution Ave NW, Washington, DC 20560, USA
| | - Marymegan Daly
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution's National Museum of Natural History, 10th and Constitution Ave NW, Washington, DC 20560, USA
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Sless TJL, Branstetter MG, Mikát M, Odanaka KA, Tobin KB, Rehan SM. Phylogenomics and biogeography of the small carpenter bees (Apidae: Xylocopinae: Ceratina). Mol Phylogenet Evol 2024; 198:108133. [PMID: 38897426 DOI: 10.1016/j.ympev.2024.108133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/31/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Small carpenter bees in the genus Ceratina are behaviourally diverse, species-rich, and cosmopolitan, with over 370 species and a range including all continents except Antarctica. Here, we present the first comprehensive phylogeny of the genus based on ultraconserved element (UCE) phylogenomic data, covering a total of 185 ingroup specimens representing 22 of the 25 current subgenera. Our results support most recognized subgenera as natural groups, but we also highlight several groups in need of taxonomic revision - particularly the nominate subgenus Ceratina sensu stricto - and several clades that likely need to be described as new subgenera. In addition to phylogeny, we explore the evolutionary history of Ceratina through divergence time estimation and biogeographic reconstruction. Our findings suggest that Ceratinini split from its sister tribe Allodapini about 72 million years ago. The common ancestor of Ceratina emerged in the Afrotropical realm approximately 42 million years ago, near the Middle Eocene Climatic Optimum. Multiple subsequent dispersal events led to the present cosmopolitan distribution of Ceratina, with the majority of transitions occurring between the Afrotropics, Indomalaya, and the Palearctic. Additional movements also led to the arrival of Ceratina in Madagascar, Australasia, and a single colonization of the Americas. Dispersal events were asymmetrical overall, with temperate regions primarily acting as destinations for migrations from tropical source regions.
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Affiliation(s)
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Logan, UT, USA
| | - Michael Mikát
- Department of Biology, York University, Toronto, ON, Canada; Department of General Zoology, Martin Luther University, Halle, Germany; Department of Zoology, Charles University, Prague, Czech Republic
| | | | - Kerrigan B Tobin
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Logan, UT, USA; Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, ON, Canada.
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4
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González-Delgado S, Rodríguez-Flores PC, Giribet G. Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia). Mol Phylogenet Evol 2024; 198:108129. [PMID: 38878989 DOI: 10.1016/j.ympev.2024.108129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/15/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.
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Affiliation(s)
- Sara González-Delgado
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Santa Cruz de Tenerife, Canary Islands, Spain; Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paula C Rodríguez-Flores
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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Christodoulides N, Urgiles VL, Guayasamin JM, Savage AE. Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus. Genome Biol Evol 2024; 16:evae167. [PMID: 39109890 PMCID: PMC11342244 DOI: 10.1093/gbe/evae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2024] [Indexed: 08/24/2024] Open
Abstract
The genus Pristimantis diversified in the tropical Andes mountains and is the most speciose genus of terrestrial vertebrates. Pristimantis are notable among frogs in that they thrive at high elevations (>2,000 m) and are direct developers without a tadpole stage. Despite their ecological significance, little is known about the genetic and physiological traits enabling their success. We conducted transcriptomic analysis on seven Pristimantis species sampled across elevations in the Ecuadorean Andes to explore three hypotheses for their success: (i) unique genes are under selection relative to all other frogs, (ii) common selection occurs across all direct developers, or (iii) common selection occurs across all high-elevation frog clades. Comparative analysis with 34 frog species revealed unique positive selection in Pristimantis genes related to aerobic respiration, hemostasis, signaling, cellular transportation of proteins and ions, and immunity. Additionally, we detected positive selection across all direct developers for genes associated with oxygenase activity and metal ion binding. While many genes under selection in Pristimantis were not positively selected in other high-elevation frog species, we identified some shared genes and pathways linked to lipid metabolism, innate immunity, and cellular redox processes. We observed more positive selection in duplicated- versus single-copy genes, while relaxed purifying selection was prevalent in single-copy genes. Notably, copy number of an innate immunity complement gene was positively correlated with Pristimantis species elevation. Our findings contribute novel insights into the genetic basis of adaptation in Pristimantis and provide a foundation for future studies on the evolutionary mechanisms leading to direct development and coping with high elevations.
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Affiliation(s)
| | - Veronica L Urgiles
- Department of Biology, University of Central Florida, Orlando, FL, USA
- Departamento de herpetologia, Instituto Nacional de Biodiversidad del Ecuador, Quito, Ecuador
| | - Juan M Guayasamin
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto Biósfera, Laboratorio de Biología Evolutiva, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Ingeniería en Biodiversidad y Recursos Genéticos, Centro de Biodiversidad y Cambio Climático BioCamb, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Anna E Savage
- Department of Biology, University of Central Florida, Orlando, FL, USA
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Bernauer OM, Branstetter MG, Cook JM, Tierney SM. Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop. BMC Ecol Evol 2024; 24:104. [PMID: 39095704 PMCID: PMC11295329 DOI: 10.1186/s12862-024-02293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either 'natural' or 'disturbed' landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion. RESULTS A phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3-0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE. CONCLUSIONS Bee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.
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Affiliation(s)
- Olivia M Bernauer
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
- Department of Entomology, University of Wisconsin-Madison, 1630 Linden Dr. Madison, Madison, WI, 53706, USA.
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Utah State University, 5310 Old Main Hill, Logan, UT, 84322, USA
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Simon M Tierney
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
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Shimbori EM, Castañeda-Osorio R, Jasso-Martínez JM, Penteado-Dias AM, Gadelha SS, Brady SG, Quicke DLJ, Kula RR, Zaldívar-Riverón A. UCE-based phylogenomics of the lepidopteran endoparasitoid wasp subfamily Rogadinae (Hymenoptera: Braconidae) unveils a new Neotropical tribe. INVERTEBR SYST 2024; 38:IS24040. [PMID: 39116275 DOI: 10.1071/is24040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
During the past two decades, the phylogenetic relationships and higher-level classification of the subfamily Rogadinae have received relevant contributions based on Sanger, mitogenome and genome-wide nuclear DNA sequence data. These studies have helped to update the circumscription and tribal classification of this subfamily, with six tribes currently recognised (Aleiodini, Betylobraconini, Clinocentrini, Rogadini, Stiropiini and Yeliconini). The tribal relationships within Rogadinae, however, are yet to be fully resolved, including the status of tribe Facitorini, previously regarded as betylobraconine, with respect to the members of Yeliconini. We conducted a phylogenomic analysis among the tribes of Rogadinae based on genomic ultraconserved element (UCE) data and extensive taxon sampling including three undescribed genera of uncertain tribal placement. Our almost fully supported estimate of phylogeny confirmed the basal position of Rogadini within the subfamily and a Facitorini clade (Yeliconini+Aleiodini) that led us to propose the former group as a valid rogadine tribe (Facitorini stat. res.). Stiropiini, however, was recovered for the first time as sister to the remaining rogadine tribes except Rogadini, and Clinocentrini as sister to a clade with Betylobraconini+the three undescribed genera. The relationships recovered and morphological examination of the material included led us to place the latter three new genera and recently described genus Gondwanocentrus within a new rogadine tribe, Gondwanocentrini Shimbori & Zaldívar-Riverón trib. nov. We described these genera (Ghibli Shimbori & Zaldívar-Riverón gen. nov., Racionais Shimbori & Zaldívar-Riverón gen. nov. and Soraya Shimbori gen. nov.) with two or three new species each (G. miyazakii Shimbori & Zaldívar-Riverón sp. nov., G. totoro Shimbori & Zaldívar-Riverón sp. nov., R. brunus Shimbori & Zaldívar-Riverón sp. nov., R. kaelejay Shimbori & Zaldívar-Riverón sp. nov., R. superstes Shimbori & Zaldívar-Riverón sp. nov., S. alencarae Shimbori sp. nov. and S. venus Shimbori & Zaldívar-Riverón sp. nov.). A new species of Facitorini, Jannya pasargadae Gadelha & Shimbori sp. nov., is also described. Our newly proposed classification expands the number of tribes and genera within Rogadinae to 8 and 66 respectively. ZooBank: urn:lsid:zoobank.org:pub:51951C78-069A-4D8B-B5F0-7EBD4D9D21CE.
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Affiliation(s)
- Eduardo M Shimbori
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico; and Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil; and Centre de coopération internationale en recherche agronomique pour lle développement (CIRAD), Centre de Biologie pour la Gestion de Populations (CBGP), Montpellier, F-34398, France; and CIRAD, CBGP, Institute National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAe), Institut Agro, Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Rubén Castañeda-Osorio
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Jovana M Jasso-Martínez
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico; and Department of Entomology, Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue NW, Washington, DC 20560, USA
| | - Angélica M Penteado-Dias
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Sian S Gadelha
- Laboratório de Biologia e Diversidade de Insetos, Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | - Seán G Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue NW, Washington, DC 20560, USA
| | - Donald L J Quicke
- Integrative Insect Ecology Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Robert R Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, c/o Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Zheng S, Zhang C, Zhou J, Zhang S, Liu Y, Jin X, Wang Y, Liu B. Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda. Biochem Genet 2024; 62:3030-3051. [PMID: 38063953 DOI: 10.1007/s10528-023-10594-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 07/31/2024]
Abstract
In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.
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Affiliation(s)
- Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China.
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China.
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9
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Joele FR, Dias Filho MM, Jasso-Martínez JM, Garzón-Orduña IJ. Phylogenomics of the geometrid tribe Palyadini (Lepidoptera: Geometridae) reveals contrasting patterns of phylogenetic signal in wing colour characters. Cladistics 2024; 40:374-390. [PMID: 38532274 DOI: 10.1111/cla.12574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 03/28/2024] Open
Abstract
Next generation sequencing techniques currently represent a practical and efficient way to infer robust evolutionary hypotheses. Palyadini is a small Neotropical tribe of geometrid moths composed of six genera that feature strikingly colourful wings. Here, we investigated patterns of evolution and amount of phylogenetic signal contained in various colour characters featured in the wings of members of this tribe by (i) inferring a robust phylogenetic hypothesis using ultraconserved elements (UCEs), and afterwards, (ii) mapping the morphological characters onto the molecular topology under a parsimonious ancestral character optimization. Our matrix, obtained with 60% completeness, includes 754 UCE loci and 73 taxa (64 ingroup, nine outgroup). Maximum likelihood and parsimony generated largely identical topologies with strongly supported nodes, except for one node inside the genus Opisthoxia. According to our topology, most wing colour characters are reconstructed as homoplastic, particularly at the tribe level, but five of the seven provide evidence supporting common ancestry at the genus level. Our results emphasize, once again, that no character system is infallible, and that more research is necessary to take our understanding of the evolution of wing colour in moths to a level comparable with the knowledge we have for butterflies.
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Affiliation(s)
- Flávia R Joele
- Laboratorio de Sistemática de Polillas, Departamento de Zoología, Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Cto. Zona Deportiva S/N, C.U. Coyocan., CDMX, 04510, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, 1° Piso. Circuito de Posgrados, CU. Coyoacan, CDMX, 04510, Mexico
| | - Manoel M Dias Filho
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, Rod. Washington Luís, s/n - Monjolinho., Sao Carlos, 13565-905, Brazil
| | - Jovana M Jasso-Martínez
- Departamento de Zoología, Colección Nacional de Insectos Instituto de Biología, UNAM, Cto. Zona Deportiva S/N, C.U. Coyocan., CDMX, 04510, Mexico
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, 20560, USA
| | - Ivonne J Garzón-Orduña
- Laboratorio de Sistemática de Polillas, Departamento de Zoología, Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Cto. Zona Deportiva S/N, C.U. Coyocan., CDMX, 04510, Mexico
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10
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Santos BF, Colombo WD, Murray EA, Brady SG, Azevedo CO. Insights from the first phylogenomic analysis of flat wasps (Hymenoptera, Bethylidae) reveal two new subfamilies. Cladistics 2024. [PMID: 39056213 DOI: 10.1111/cla.12594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/14/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Despite significant advances in alpha level taxonomy in the past few decades, the higher-level phylogeny of flat wasps (Hymenoptera, Bethylidae) remains poorly explored. Herein we provide the first phylogenomic assessment of the family based on data from ultraconserved elements for 96 species in 61 genera of the family, with material from 29 countries and all biogeographic regions. Dataset cutoffs including ultraconserved element loci recovered for 50 and 70% of terminals resulted in matrices with 1513 and 451 loci, which were analysed in both parsimony and maximum likelihood frameworks. We also provide the first analyses of divergence dating for the family based on the calibration of 12 nodes. All analyses recovered the Bethylidae as a monophyletic group and estimated the origin of the family at around 143 Ma. The results suggest that all extant subfamilies had already diversified by the Late Cretaceous. All topologies suggest that Glenosema and Chilepyris form a clade separate from other Scleroderminae; owing to the morphological distinctiveness of each genus, we propose that they are accommodated in two new subfamilies, Glenoseminae subf. nov. and Chilepyrinae subf. nov. The monotypic sclerodermine genus Galodoxa was consistently recovered within Epyrinae and is transferred to the latter subfamily.
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Affiliation(s)
- Bernardo F Santos
- Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Invalidenstraße 43, Berlin, 10115, Germany
| | - Wesley D Colombo
- Depto de Ciências Biológicas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari 514, Goiabeiras, Vitória, 29075-010, ES, Brazil
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, 10th and Constitution Ave. NW, Washington, DC, USA
| | - Celso O Azevedo
- Depto de Ciências Biológicas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari 514, Goiabeiras, Vitória, 29075-010, ES, Brazil
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11
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Wang Y, Chen GC, Wang Z, Luo K, Zhang Y, Li Y, McClain AC, Jankowska MM, Perreira KM, Mattei J, Isasi CR, Llabre MM, Thyagarajan B, Daviglus ML, Van Horn L, Goldsztajn Farelo D, Maldonado LE, Levine SR, Yu B, Boerwinkle E, Knight R, Burk RD, Kaplan RC, Qi Q, Peters BA. Dietary Acculturation Is Associated With Altered Gut Microbiome, Circulating Metabolites, and Cardiovascular Disease Risk in US Hispanics and Latinos: Results From HCHS/SOL. Circulation 2024; 150:215-229. [PMID: 39008559 DOI: 10.1161/circulationaha.124.069824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/10/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Dietary acculturation, or adoption of dominant culture diet by migrant groups, influences human health. We aimed to examine dietary acculturation and its relationships with cardiovascular disease (CVD), gut microbiota, and blood metabolites among US Hispanic and Latino adults. METHODS In the HCHS/SOL (Hispanic Community Health Study/Study of Latinos), US exposure was defined by years in the United States (50 states and Washington, DC) and US nativity. A dietary acculturation pattern was derived from 14 172 participants with two 24-hour dietary recalls at baseline (2008-2011) using least absolute shrinkage and selection operator regression, with food groups as predictors of US exposure. We evaluated associations of dietary acculturation with incident CVD across ≈7 years of follow-up (n=211/14 172 cases/total) and gut microbiota (n=2349; visit 2, 2014 to 2017). Serum metabolites associated with both dietary acculturation-related gut microbiota (n=694) and incident CVD (n=108/5256 cases/total) were used as proxy measures to assess the association of diet-related gut microbiome with incident CVD. RESULTS We identified an empirical US-oriented dietary acculturation score that increased with US exposure. Higher dietary acculturation score was associated with higher risk of incident CVD (hazard ratio per SD, 1.33 [95% CI, 1.13-1.57]), adjusted for sociodemographic, lifestyle, and clinical factors. Sixty-nine microbial species (17 enriched from diverse species, 52 depleted mainly from fiber-utilizing Clostridia and Prevotella species) were associated with dietary acculturation, driven by lower intakes of whole grains, beans, and fruits and higher intakes of refined grains. Twenty-five metabolites, involved predominantly in fatty acid and glycerophospholipid metabolism (eg, branched-chain 14:0 dicarboxylic acid** and glycerophosphoethanolamine), were associated with both diet acculturation-related gut microbiota and incident CVD. Proxy association analysis based on these metabolites suggested a positive relationship between diet acculturation-related microbiome and risk of CVD (r=0.70, P<0.001). CONCLUSIONS Among US Hispanic and Latino adults, greater dietary acculturation was associated with elevated CVD risk, possibly through alterations in gut microbiota and related metabolites. Diet and microbiota-targeted interventions may offer opportunities to mitigate CVD burdens of dietary acculturation.
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Affiliation(s)
- Yi Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Guo-Chong Chen
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
- Department of Nutrition and Food Hygiene, School of Public Health, Suzhou Medical College of Soochow University, China (G.-C.C.)
| | - Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Kai Luo
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Yanbo Zhang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Yang Li
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Amanda C McClain
- School of Exercise and Nutritional Sciences, San Diego State University, CA (A.C.M.)
| | - Marta M Jankowska
- Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA (M.M.J.)
| | - Krista M Perreira
- Department of Social Medicine, University of North Carolina at Chapel Hill (K.M.P.)
| | - Josiemer Mattei
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA (J.M.)
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Maria M Llabre
- Department of Psychology, University of Miami, FL (M.M.L.)
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis (B.T.)
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois Chicago (M.L.D.)
| | - Linda Van Horn
- Department of Preventive Medicine, Northwestern University, Chicago, IL (L.V.H.)
| | | | - Luis E Maldonado
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles (L.E.M.)
| | - Steven R Levine
- SUNY Downstate Health Sciences University, Brooklyn, NY (S.R.L.)
| | - Bing Yu
- Department of Epidemiology (B.Y.), School of Public Health, University of Texas Health Science Center at Houston, Houston
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences (E.B.), School of Public Health, University of Texas Health Science Center at Houston, Houston
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, Bioengineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla (R.K.)
| | - Robert D Burk
- Departments of Pediatrics, Microbiology & Immunology, and Obstetrics, Gynecology & Women's Health, Albert Einstein College of Medicine, Bronx, NY(R.D.B.)
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (R.C.K.)
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY (Y.W., G.-C.C., Z.W., K.L., Y.Z., Y.L., C.R.I., R.D.B., R.C.K., Q.Q., B.A.P.)
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12
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Gómez-Bravo A, Cirignoli S, Wehrendt D, Schijman A, León CM, Flores-Chaves M, Nieto J, Kieran TJ, Abril M, Guhl F. Zoonotic Cycle of American Trypanosomiasis in an Endemic Region of the Argentine Chaco, Factors That Influenced a Paradigm Shift. INSECTS 2024; 15:471. [PMID: 39057204 PMCID: PMC11277326 DOI: 10.3390/insects15070471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/16/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease (American trypanosomiasis), is a highly complex zoonosis that is present throughout South America, Central America, and Mexico. The transmission of this disease is influenced by various factors, including human activities like deforestation and land use changes, which may have altered the natural transmission cycles and their connection to the environment. In this study conducted in the Argentine Chaco region, we examined the transmission dynamics of T. cruzi by collecting blood samples from wild and domestic animals, as well as triatomine bugs from human dwellings, across five sites of varying anthropic intervention. Samples were analyzed for T. cruzi infection via qPCR, and we additionally examined triatomines for bloodmeal analysis via NGS amplicon sequencing. Our analysis revealed a 15.3% infection rate among 20 wild species (n = 123) and no T. cruzi presence in 9 species of domestic animals (n = 1359) or collected triatomines via qPCR. Additionally, we found chicken (34.28%), human (21.59%), and goat (19.36%) as the predominant bloodmeal sources across all sites. These findings suggest that anthropic intervention and other variables analyzed may have directly impacted the spillover dynamics of T. cruzi's sylvatic cycle and potentially reduced its prevalence in human habitats.
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Affiliation(s)
- Andrea Gómez-Bravo
- Fundación Mundo Sano, Buenos Aires C1061ABC, Argentina; (A.G.-B.); (M.F.-C.); (M.A.)
| | - Sebastián Cirignoli
- Centro de Investigaciones del Bosque Atlántico, Puerto Iguazú N3370AIA, Argentina;
- Administración de Parques Nacionales, Parque Nacional Iberá, Mercedes W3470, Argentina
| | - Diana Wehrendt
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Buenos Aires C1428ADN, Argentina; (D.W.); (A.S.)
| | - Alejandro Schijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Buenos Aires C1428ADN, Argentina; (D.W.); (A.S.)
| | - Cielo M. León
- Centro de Investigaciones en Microbiología y Parasitología Tropical, Universidad de los Andes, Bogotá 111711, Colombia;
| | - María Flores-Chaves
- Fundación Mundo Sano, Buenos Aires C1061ABC, Argentina; (A.G.-B.); (M.F.-C.); (M.A.)
- Unidad de Leishmaniasis y Enfermedad de Chagas, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28222 Majadahonda, Spain;
| | - Javier Nieto
- Unidad de Leishmaniasis y Enfermedad de Chagas, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28222 Majadahonda, Spain;
| | - Troy J. Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, USA;
| | - Marcelo Abril
- Fundación Mundo Sano, Buenos Aires C1061ABC, Argentina; (A.G.-B.); (M.F.-C.); (M.A.)
| | - Felipe Guhl
- Centro de Investigaciones en Microbiología y Parasitología Tropical, Universidad de los Andes, Bogotá 111711, Colombia;
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13
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Talbot SC, Vining KJ, Snelling JW, Clevenger J, Mehlenbacher SA. A haplotype-resolved chromosome-level assembly and annotation of European hazelnut (C. avellana cv. Jefferson) provides insight into mechanisms of eastern filbert blight resistance. G3 (BETHESDA, MD.) 2024; 14:jkae021. [PMID: 38325326 DOI: 10.1093/g3journal/jkae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
European hazelnut (Corylus avellana L.) is an important tree nut crop. Hazelnut production in North America is currently limited in scalability due to Anisogramma anomala, a fungal pathogen that causes Eastern Filbert Blight (EFB) disease in hazelnut. Successful deployment of EFB resistant cultivars has been limited to the state of Oregon, where the breeding program at Oregon State University (OSU) has released cultivars with a dominant allele at a single resistance locus identified by classical breeding, linkage mapping, and molecular markers. C. avellana cultivar "Jefferson" is resistant to the predominant EFB biotype in Oregon and has been selected by the OSU breeding program as a model for hazelnut genetic and genomic research. Here, we present a near complete, haplotype-resolved chromosome-level hazelnut genome assembly for "Jefferson". This new assembly is a significant improvement over a previously published genome draft. Analysis of genomic regions linked to EFB resistance and self-incompatibility confirmed haplotype splitting and identified new gene candidates that are essential for downstream molecular marker development, thereby facilitating breeding efforts.
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Affiliation(s)
- Samuel C Talbot
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Kelly J Vining
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Jacob W Snelling
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Josh Clevenger
- Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Shawn A Mehlenbacher
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
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14
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Brownstein CD, Zapfe KL, Lott S, Harrington R, Ghezelayagh A, Dornburg A, Near TJ. Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean. Curr Biol 2024; 34:2541-2550.e4. [PMID: 38788708 DOI: 10.1016/j.cub.2024.04.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Major ecological transitions are thought to fuel diversification, but whether they are contingent on the evolution of certain traits called key innovations1 is unclear. Key innovations are routinely invoked to explain how lineages rapidly exploit new ecological opportunities.1,2,3 However, investigations of key innovations often focus on single traits rather than considering trait combinations that collectively produce effects of interest.4 Here, we investigate the evolution of synergistic trait interactions in anglerfishes, which include one of the most species-rich vertebrate clades in the bathypelagic, or "midnight," zone of the deep sea: Ceratioidea.5 Ceratioids are the only vertebrates that possess sexual parasitism, wherein males temporarily attach or permanently fuse to females to mate.6,7 We show that the rapid transition of ancestrally benthic anglerfishes into pelagic habitats occurred during a period of major global warming 50-35 million years ago.8,9 This transition coincided with the origins of sexual parasitism, which is thought to increase the probability of successful reproduction once a mate is found in the midnight zone, Earth's largest habitat.5,6,7 Our reconstruction of the evolutionary history of anglerfishes and the loss of immune genes support that permanently fusing clades have convergently degenerated their adaptive immunity. We find that degenerate adaptive immune genes and sexual body size dimorphism, both variably present in anglerfishes outside the ceratioid radiation, likely promoted their transition into the bathypelagic zone. These results show how traits from separate physiological, morphological, and reproductive systems can interact synergistically to drive major transitions and subsequent diversification in novel environments.
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Affiliation(s)
- Chase D Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Katerina L Zapfe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Spencer Lott
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
| | - Richard Harrington
- Department of Natural Resources, Marine Resources Division, 217 Ft. Johnson Road, Charleston, SC 29412-9110, USA
| | - Ava Ghezelayagh
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA; Peabody Museum, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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15
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Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen KN, Bhuiyan M, Brunelle B, Robinson G, Chalmers RM, Alves-Ferreira E, Grigg ME, Kissinger JC, Glenn TC. WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp. RESEARCH SQUARE 2024:rs.3.rs-4294842. [PMID: 38798642 PMCID: PMC11118713 DOI: 10.21203/rs.3.rs-4294842/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
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Affiliation(s)
- N J Bayona-Vásquez
- Division of Natural Science and Mathematics, Oxford College of Emory University, Oxford, GA, 30054, USA
| | - A H Sullivan
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - M S Beaudry
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - A Khan
- Animal Parasitic Disease Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - R P Baptista
- Infectious Diseases, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - K N Petersen
- Odum School of Ecology, University of Georgia, University of Georgia, Athens, GA, 30602, USA
| | - Miu Bhuiyan
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
| | - B Brunelle
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - G Robinson
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - R M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales, Microbiology and Health Protection, Singleton Hospital, Swansea SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - Evc Alves-Ferreira
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M E Grigg
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - T C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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16
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Palacios N, Gordon S, Wang T, Burk R, Qi Q, Huttenhower C, Gonzalez HM, Knight R, De Carli C, Daviglus M, Lamar M, Telavera G, Tarraf W, Kosciolek T, Cai J, Kaplan RC. Gut Microbiome Multi-Omics and Cognitive Function in the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.17.24307533. [PMID: 38798527 PMCID: PMC11118626 DOI: 10.1101/2024.05.17.24307533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
INTRODUCTION We conducted a study within the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging (HCHS/SOL-INCA) cohort to examine the association between gut microbiome and cognitive function. METHODS We analyzed the fecal metagenomes of 2,471 HCHS/SOL-INCA participants to, cross-sectionally, identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition. RESULTS Eubacterium species( E. siraeum and E. eligens ), were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition. DISCUSSION In a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.
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17
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Castañeda-Osorio R, Belokobylskij SA, Jasso-Martínez JM, Samacá-Sáenz E, Kula RR, Zaldívar-Riverón A. Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics. INVERTEBR SYST 2024; 38:IS24029. [PMID: 38740060 DOI: 10.1071/is24029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.
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Affiliation(s)
- Rubén Castañeda-Osorio
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er Piso, Circuito de Posgrados, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sergey A Belokobylskij
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, Saint Petersburg, Russian Federation
| | - Jovana M Jasso-Martínez
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Department of Entomology, Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue NW, Washington, DC, USA
| | - Ernesto Samacá-Sáenz
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
| | - Robert R Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, c/o Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
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18
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Griffiths JA, Yoo BB, Thuy-Boun P, Cantu VJ, Weldon KC, Challis C, Sweredoski MJ, Chan KY, Thron TM, Sharon G, Moradian A, Humphrey G, Zhu Q, Shaffer JP, Wolan DW, Dorrestein PC, Knight R, Gradinaru V, Mazmanian SK. Peripheral neuronal activation shapes the microbiome and alters gut physiology. Cell Rep 2024; 43:113953. [PMID: 38517896 PMCID: PMC11132177 DOI: 10.1016/j.celrep.2024.113953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/07/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia. The GI tract also harbors a diverse microbiome, but interactions between the ENS and the microbiome remain poorly understood. Here, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated neurons in mice to determine effects on intestinal microbial communities and their metabolites as well as on host physiology. The resulting multi-omics datasets support broad roles for discrete peripheral neuronal subtypes in shaping microbiome structure, including modulating bile acid profiles and fungal colonization. Physiologically, activation of either ChAT+ or TH+ neurons increases fecal output, while only ChAT+ activation results in increased colonic contractility and diarrhea-like fluid secretion. These findings suggest that specific subsets of peripherally activated neurons differentially regulate the gut microbiome and GI physiology in mice without involvement of signals from the brain.
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Affiliation(s)
- Jessica A Griffiths
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Bryan B Yoo
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter Thuy-Boun
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Victor J Cantu
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, USA
| | - Collin Challis
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael J Sweredoski
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ken Y Chan
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Taren M Thron
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gil Sharon
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Shu Chien-Gene Lay Department of Engineering, University of California, San Diego, San Diego, CA, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA
| | - Viviana Gradinaru
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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19
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Usyk M, Hayes RB, Knight R, Gonzalez A, Li H, Osman I, Weber JS, Ahn J. Gut microbiome is associated with recurrence-free survival in patients with resected Stage IIIB-D or Stage IV melanoma treated with immune checkpoint inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589761. [PMID: 38659744 PMCID: PMC11042335 DOI: 10.1101/2024.04.16.589761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The gut microbiome (GMB) has been associated with outcomes of immune checkpoint blockade therapy in melanoma, but there is limited consensus on the specific taxa involved, particularly across different geographic regions. We analyzed pre-treatment stool samples from 674 melanoma patients participating in a phase-III trial of adjuvant nivolumab plus ipilimumab versus nivolumab, across three continents and five regions. Longitudinal analysis revealed that GMB was largely unchanged following treatment, offering promise for lasting GMB-based interventions. In region-specific and cross-region meta-analyses, we identified pre-treatment taxonomic markers associated with recurrence, including Eubacterium, Ruminococcus, Firmicutes, and Clostridium. Recurrence prediction by these markers was best achieved across regions by matching participants on GMB compositional similarity between the intra-regional discovery and external validation sets. AUCs for prediction ranged from 0.83-0.94 (depending on the initial discovery region) for patients closely matched on GMB composition (e.g., JSD ≤0.11). This evidence indicates that taxonomic markers for prediction of recurrence are generalizable across regions, for individuals of similar GMB composition.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | - Richard B. Hayes
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Rob Knight
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Antonio Gonzalez
- Departments of Pediatrics, Computer Science & Engineering, and Bioengineering; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Huilin Li
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Iman Osman
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
- The Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Jeffrey S. Weber
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Jiyoung Ahn
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
- NYU Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
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20
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Caizergues AE, Santangelo JS, Ness RW, Angeoletto F, Anstett DN, Anstett J, Baena-Diaz F, Carlen EJ, Chaves JA, Comerford MS, Dyson K, Falahati-Anbaran M, Fellowes MDE, Hodgins KA, Hood GR, Iñiguez-Armijos C, Kooyers NJ, Lázaro-Lobo A, Moles AT, Munshi-South J, Paule J, Porth IM, Santiago-Rosario LY, Whitney KS, Tack AJM, Johnson MTJ. Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant? Mol Ecol 2024; 33:e17311. [PMID: 38468155 DOI: 10.1111/mec.17311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.
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Affiliation(s)
- Aude E Caizergues
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - James S Santangelo
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Rob W Ness
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Fabio Angeoletto
- Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis, Rondonópolis, Brasil
| | - Daniel N Anstett
- Department of Plant Biology, Department of Entomology, Plant Resilience Institute, Michigan State University, East Lansing, Michigan, USA
| | - Julia Anstett
- Genomic Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elizabeth J Carlen
- Living Earth Collaborative, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jaime A Chaves
- Universidad San Francisco de Quito, Ecuador, Quito
- San Francisco State University, San Francisco, California, USA
| | - Mattheau S Comerford
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | | | | | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Glen Ray Hood
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Carlos Iñiguez-Armijos
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Universidad Técnica Particular de Loja, Loja, Ecuador
| | | | - Adrián Lázaro-Lobo
- Biodiversity Research Institute (IMIB), CSIC-University of Oviedo-Principality of Asturias, Mieres, Spain
| | - Angela T Moles
- Evolution & Ecology Research Centre, UNSW-University of New South Wales, Sydney, New South Wales, Australia
| | - Jason Munshi-South
- Department of Biology and Louis Calder Center, Fordham University, New York City, New York, USA
| | - Juraj Paule
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Ilga M Porth
- Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Luis Y Santiago-Rosario
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Kaitlin Stack Whitney
- Science, Technology & Society Department, Rochester Institute of Technology, Rochester, New York, USA
| | - Ayko J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Marc T J Johnson
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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21
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Sato S, Derkarabetian S, Valdez-Mondragón A, Pérez-González A, Benavides LR, Daniels SR, Giribet G. Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules. Mol Phylogenet Evol 2024; 193:108026. [PMID: 38341007 DOI: 10.1016/j.ympev.2024.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/14/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions. To date, only four molecular analyses have been conducted on the group and they failed to resolve the relationships of the main lineages and even recovering the non-monophyly of the three genera. These studies were limited to a few Sanger loci or phylogenomic analyses with at most seven ingroup samples. To increase phylogenetic resolution in this little-understood and poorly studied group, we present the most comprehensive phylogenomic study of Ricinulei to date leveraging the Arachnida ultra-conserved element probe set. With a data set of 473 loci across 96 ingroup samples, analyses resolved a monophyletic Neotropical clade consisting of four main lineages. Two of them correspond to the current genera Cryptocellus and Pseudocellus while topology testing revealed one lineage to likely be a phylogenetic reconstruction artefact. The fourth lineage, restricted to Northwestern, Andean South America, is consistent with the Cryptocellus magnus group, likely corresponding to the historical genus Heteroricinoides. Since we did not sample the type species for this old genus, we do not formally re-erect Heteroricinoides but our data suggest the need for a thorough morphological re-examination of Neotropical Ricinulei.
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Affiliation(s)
- Shoyo Sato
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Alejandro Valdez-Mondragón
- Collection of Arachnology (CARCIB), Programa Académico de Planeación Ambiental y Conservación (PLAYCO), Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C., La Paz, Baja California Sur, Mexico
| | - Abel Pérez-González
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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22
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Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, Méric G, Inouye M. Integration of polygenic and gut metagenomic risk prediction for common diseases. NATURE AGING 2024; 4:584-594. [PMID: 38528230 PMCID: PMC11031402 DOI: 10.1038/s43587-024-00590-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024]
Abstract
Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Shu Mei Teo
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Matti O Ruuskanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Computing, University of Turku, Turku, Finland
| | - Oleg Kambur
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Jon Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Karin Verspoor
- School of Computing Technologies, RMIT University, Melbourne, Victoria, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- The Alan Turing Institute, London, UK.
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23
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Bossert S, Pauly A, Danforth BN, Orr MC, Murray EA. Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae). Mol Ecol Resour 2024; 24:e13925. [PMID: 38183389 DOI: 10.1111/1755-0998.13925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Washington State University, Pullman, Washington, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alain Pauly
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Brussels, Belgium
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
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24
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Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen KN, Bhuiyan M, Brunelle B, Robinson G, Chalmers RM, Alves-Ferreira E, Grigg ME, AlvesFerreira Kissinger JC, Glenn TC. WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586458. [PMID: 38585809 PMCID: PMC10996700 DOI: 10.1101/2024.03.29.586458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
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25
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Salter JF, Brumfield RT, Faircloth BC. An island 'endemic' born out of hybridization between introduced lineages. Mol Ecol 2024; 33:e16990. [PMID: 37208829 DOI: 10.1111/mec.16990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 05/21/2023]
Abstract
Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human-mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human-mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human-mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human-mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages.
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Affiliation(s)
- Jessie F Salter
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Louisiana, Baton Rouge, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Louisiana, Baton Rouge, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Louisiana, Baton Rouge, USA
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26
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Burcham ZM, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Connor M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nat Microbiol 2024; 9:595-613. [PMID: 38347104 PMCID: PMC10914610 DOI: 10.1038/s41564-023-01580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/08/2023] [Indexed: 03/07/2024]
Abstract
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.
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Affiliation(s)
- Zachary M Burcham
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Animal Sciences, Auburn University, Auburn, AL, USA
| | - Bridget B McGivern
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Parsa Ghadermazi
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
- Institute for Systems Genetics, New York Grossman School of Medicine, New York University, New York, NY, USA
- Department of Computer Science, New York University, New York, NY, USA
| | - Anru R Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Pixu Shi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Alexandra Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Heather L Deel
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhenjiang Zech Xu
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Victoria Nieciecki
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Greg C Humphry
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Melissa Connor
- Forensic Investigation Research Station, Colorado Mesa University, Grand Junction, CO, USA
| | - Derek Boyd
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Department of Social, Cultural, and Justice Studies, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Jake Smith
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Mid-America College of Funeral Service, Jeffersonville, IN, USA
| | - Jenna M S Watson
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Giovanna Vidoli
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Dawnie Steadman
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Aaron M Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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27
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Starrett J, Jochim EE, Quayle IL, Zahnle XJ, Bond JE. Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.). Ecol Evol 2024; 14:e10983. [PMID: 38435003 PMCID: PMC10905247 DOI: 10.1002/ece3.10983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider, Promyrmekiaphila korematsui sp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genus Promyrmekiaphila and its constituent species, which also includes P. clathrata and P. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages within P. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into close contact. Alternatively, phenotypic cohesion among genetically divergent P. clathrata lineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence in Promyrmekiaphila at the population-species interface.
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28
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Youk J, Kwon HW, Lim J, Kim E, Kim T, Kim R, Park S, Yi K, Nam CH, Jeon S, An Y, Choi J, Na H, Lee ES, Cho Y, Min DW, Kim H, Kang YR, Choi SH, Bae MJ, Lee CG, Kim JG, Kim YS, Yu T, Lee WC, Shin JY, Lee DS, Kim TY, Ku T, Kim SY, Lee JH, Koo BK, Lee H, Yi OV, Han EC, Chang JH, Kim KS, Son TG, Ju YS. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. CELL GENOMICS 2024; 4:100499. [PMID: 38359788 PMCID: PMC10879144 DOI: 10.1016/j.xgen.2024.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1 Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Woo Kwon
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joonoh Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Eunji Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 20, Boramae-ro 5 Gil, Dongjak-gu, Seoul 07061, Republic of Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sara Jeon
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jinwook Choi
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Hyelin Na
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Youngwon Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Dong-Wook Min
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - HyoJin Kim
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Min Ji Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Chang Geun Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Joon-Goon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Tosol Yu
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Dongnam Institute of Radiological and Medical Science, Busan 46033, Republic of Korea
| | | | | | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - On Vox Yi
- Department of Breast Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Eon Chul Han
- Department of Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyung Su Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA.
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29
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Nguyen HDT, Ponomareva E, Dadej K, Smith D, Antoun M, van der Lee TAJ, van de Vossenberg BTLH. A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences. PLoS One 2024; 19:e0296842. [PMID: 38346034 PMCID: PMC10861067 DOI: 10.1371/journal.pone.0296842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/19/2023] [Indexed: 02/15/2024] Open
Abstract
Potato wart disease is caused by the obligate fungal pathogen Synchytrium endobioticum. DNA extraction from compost, purified spores and crude wart tissue derived from tuber galls of infected potatoes often results in low S. endobioticum DNA concentration or highly contaminated with DNA coming from other microorganisms and the potato host. Therefore, Illumina sequencing of these samples generally results in suboptimal recovery of the nuclear genome sequences of S. endobioticum. A hybridization-based target enrichment protocol was developed to strongly enhance the recovery of S. endobioticum DNA while off-target organisms DNA remains uncaptured. The design strategy involved creating a set of 180,000 molecular baits targeting both gene and non-gene regions of S. endobioticum. The baits were applied to whole genome amplified DNA samples of various S. endobioticum pathotypes (races) in compost, from purified spores and crude wart tissue samples. This was followed by Illumina sequencing and bioinformatic analyses. Compared to non-enriched samples, target enriched samples: 1) showed a significant increase in the proportion of sequenced bases mapped to the S. endobioticum nuclear genome, especially for crude wart tissue samples; 2) yielded sequencing data with higher and better nuclear genome coverage; 3) biased genome assembly towards S. endobioticum sequences, yielding smaller assembly sizes but higher representation of putative S. endobioticum contigs; 4) showed an increase in the number of S. endobioticum genes detected in the genome assemblies. Our hybridization-based target enrichment protocol offers a valuable tool for enhancing genome sequencing and NGS-based molecular detection of S. endobioticum, especially in difficult samples.
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Affiliation(s)
- Hai D. T. Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ekaterina Ponomareva
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kasia Dadej
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Donna Smith
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Prince Edward Island, Canada
| | - Melissa Antoun
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, Prince Edward Island, Canada
| | - Theo A. J. van der Lee
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen, The Netherlands
| | - Bart T. L. H. van de Vossenberg
- Netherlands Institute for Vectors, Invasive Plants and Plant Health, Dutch National Plant Protection Organization, Wageningen, the Netherlands
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30
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Garcia CR, Norfolk WA, Howard AK, Glatter AL, Beaudry MS, Mallis NA, Welton M, Glenn TC, Lipp EK, Ottesen EA. Long-term gut colonization with ESBL-producing Escherichia coli in participants without known risk factors from the southeastern United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.03.24302254. [PMID: 38370669 PMCID: PMC10871458 DOI: 10.1101/2024.02.03.24302254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified as Escherichia coli. Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a blaCTX-M gene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two different E. coli sequence types that carried blaCTX-M-1 genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation of E. coli on media without antibiotics revealed that ESBL-E. coli typically made up a minor fraction of the overall gut E. coli population, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.
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Affiliation(s)
| | - William A. Norfolk
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Center for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amanda K. Howard
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Amanda L. Glatter
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Megan S. Beaudry
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Nicholas A. Mallis
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Michael Welton
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Travis C. Glenn
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
| | - Erin K. Lipp
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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Koponen K, Kambur O, Joseph B, Ruuskanen MO, Jousilahti P, Salido R, Brennan C, Jain M, Meric G, Inouye M, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V. Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-A Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort. Arterioscler Thromb Vasc Biol 2024; 44:477-487. [PMID: 37970720 PMCID: PMC10805357 DOI: 10.1161/atvbaha.123.319458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND Dyslipidemia is treated effectively with statins, but treatment has the potential to induce new-onset type-2 diabetes. Gut microbiota may contribute to this outcome variability. We assessed the associations of gut microbiota diversity and composition with statins. Bacterial associations with statin-associated new-onset type-2 diabetes (T2D) risk were also prospectively evaluated. METHODS We examined shallow-shotgun-sequenced fecal samples from 5755 individuals in the FINRISK-2002 population cohort with a 17+-year-long register-based follow-up. Alpha-diversity was quantified using Shannon index and beta-diversity with Aitchison distance. Species-specific differential abundances were analyzed using general multivariate regression. Prospective associations were assessed with Cox regression. Applicable results were validated using gradient boosting. RESULTS Statin use associated with differing taxonomic composition (R2, 0.02%; q=0.02) and 13 differentially abundant species in fully adjusted models (MaAsLin; q<0.05). The strongest positive association was with Clostridium sartagoforme (β=0.37; SE=0.13; q=0.02) and the strongest negative association with Bacteroides cellulosilyticus (β=-0.31; SE=0.11; q=0.02). Twenty-five microbial features had significant associations with incident T2D in statin users, of which only Bacteroides vulgatus (HR, 1.286 [1.136-1.457]; q=0.03) was consistent regardless of model adjustment. Finally, higher statin-associated T2D risk was seen with [Ruminococcus] torques (ΔHRstatins, +0.11; q=0.03), Blautia obeum (ΔHRstatins, +0.06; q=0.01), Blautia sp. KLE 1732 (ΔHRstatins, +0.05; q=0.01), and beta-diversity principal component 1 (ΔHRstatin, +0.07; q=0.03) but only when adjusting for demographic covariates. CONCLUSIONS Statin users have compositionally differing microbiotas from nonusers. The human gut microbiota is associated with incident T2D risk in statin users and possibly has additive effects on statin-associated new-onset T2D risk.
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Affiliation(s)
- Kari Koponen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
| | - Oleg Kambur
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
| | - Bijoy Joseph
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
| | | | - Pekka Jousilahti
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
| | - Rodolfo Salido
- Department of Pediatrics (R.S., C.B., R.K.), University of California San Diego, La Jolla
- Department of Bioengineering (R.S., R.K.), University of California San Diego, La Jolla
| | - Caitriona Brennan
- Department of Pediatrics (R.S., C.B., R.K.), University of California San Diego, La Jolla
| | - Mohit Jain
- Department of Medicine and Pharmacology (M.J.), University of California San Diego, La Jolla
| | - Guillaume Meric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia (G.M., M.I.)
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia (G.M.)
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia (G.M., M.I.)
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, United Kingdom (M.I.)
| | - Leo Lahti
- Department of Computing, University of Turku, Finland (M.O.R., L.L.)
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
- Department of Medicine, Turku University Hospital and University of Turku, Finland (T.N.)
| | - Aki S. Havulinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
- Institute for Molecular Medicine Finland, FiMM-HiLIFE, Helsinki, Finland (A.S.H.)
| | - Rob Knight
- Department of Pediatrics (R.S., C.B., R.K.), University of California San Diego, La Jolla
- Department of Bioengineering (R.S., R.K.), University of California San Diego, La Jolla
- Department of Computer Science and Engineering (R.K.), University of California San Diego, La Jolla
- Center for Microbiome Innovation (R.K.), University of California San Diego, La Jolla
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland (K.K., O.K., B.J., P.J., T.N., A.S.H., V.S.)
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Peters BA, Hanna DB, Wang Y, Weber KM, Topper E, Appleton AA, Sharma A, Hodis HN, Santoro N, Guillemette C, Caron P, Knight R, Burk RD, Kaplan RC, Qi Q. Sex Hormones, the Stool Microbiome, and Subclinical Atherosclerosis in Women With and Without HIV. J Clin Endocrinol Metab 2024; 109:483-497. [PMID: 37643897 PMCID: PMC11032255 DOI: 10.1210/clinem/dgad510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
CONTEXT Cardioprotective roles of endogenous estrogens may be particularly important in women with HIV, who have reduced estrogen exposure and elevated cardiovascular disease risk. The gut microbiome metabolically interacts with sex hormones, but little is known regarding possible impact on cardiovascular risk. OBJECTIVE To analyze potential interplay of sex hormones and gut microbiome in cardiovascular risk. METHODS Among 197 postmenopausal women in the Women's Interagency HIV Study, we measured 15 sex hormones in serum and assessed the gut microbiome in stool. Presence of carotid artery plaque was determined (B-mode ultrasound) in a subset (n = 134). We examined associations of (i) sex hormones and stool microbiome, (ii) sex hormones and plaque, and (iii) sex hormone-related stool microbiota and plaque, adjusting for potential confounders. RESULTS Participant median age was 58 years and the majority were living with HIV (81%). Sex hormones (estrogens, androgens, and adrenal precursors) were associated with stool microbiome diversity and specific species, similarly in women with and without HIV. Estrogens were associated with higher diversity, higher abundance of species from Alistipes, Collinsella, Erysipelotrichia, and Clostridia, and higher abundance of microbial β-glucuronidase and aryl-sulfatase orthologs, which are involved in hormone metabolism. Several hormones were associated with lower odds of carotid artery plaque, including dihydrotestosterone, 3α-diol-17G, estradiol, and estrone. Exploratory mediation analysis suggested that estrone-related species, particularly from Collinsella, may mediate the protective association of estrone with plaque. CONCLUSION Serum sex hormones are significant predictors of stool microbiome diversity and composition. The gut microbiome may play a role in estrogen-related cardiovascular protection.
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Affiliation(s)
- Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yi Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kathleen M Weber
- Cook County Health/Hektoen Institute of Medicine, Chicago, IL 60608, USA
| | - Elizabeth Topper
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Allison A Appleton
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, NY 12144, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Howard N Hodis
- Departments of Medicine and Population and Public Health Sciences, Atherosclerosis Research Unit, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nanette Santoro
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chantal Guillemette
- Centre Hospitalier Universitaire (CHU) de Québec—Université Laval Research Center, Cancer research center (CRC) and Faculty of Pharmacy, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Patrick Caron
- Centre Hospitalier Universitaire (CHU) de Québec—Université Laval Research Center, Cancer research center (CRC) and Faculty of Pharmacy, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, Bioengineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Departments of Microbiology and Immunology and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Latz MAC, Andersson A, Brugel S, Hedblom M, Jurdzinski KT, Karlson B, Lindh M, Lycken J, Torstensson A, Andersson AF. A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea. Sci Data 2024; 11:18. [PMID: 38168085 PMCID: PMC10761891 DOI: 10.1038/s41597-023-02825-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.
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Affiliation(s)
- Meike A C Latz
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.
- University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg C, Denmark.
| | - Agneta Andersson
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Sonia Brugel
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Mikael Hedblom
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Krzysztof T Jurdzinski
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Bengt Karlson
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Västra Frölunda, Sweden
| | - Markus Lindh
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Jenny Lycken
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Anders Torstensson
- Swedish Meteorological and Hydrological Institute, Community Planning Services - Oceanography, Västra Frölunda, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.
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Diaz-Suarez A, Noreikiene K, Kahar S, Ozerov MY, Gross R, Kisand V, Vasemägi A. DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems. Int J Parasitol 2024; 54:33-46. [PMID: 37633409 DOI: 10.1016/j.ijpara.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 08/28/2023]
Abstract
Eye flukes (Diplostomidae) are diverse and abundant trematode parasites that form multi-species communities in fish with negative effects on host fitness and survival. However, the environmental factors and host-related characteristics that determine species diversity, composition, and coexistence in such communities remain poorly understood. Here, we developed a cost-effective cox1 region-specific DNA metabarcoding approach to characterize parasitic diplostomid communities in two common fish species (Eurasian perch and common roach) collected from seven temperate lakes in Estonia. We found considerable inter- and intra-lake, as well as inter-host species, variation in diplostomid communities. Sympatric host species characterization revealed that parasite communities were typically more diverse in roach than perch. Additionally, we detected five positive and two negative diplostomid species associations in roach, whereas only a single negative association was observed in perch. These results indicate that diplostomid communities in temperate lakes are complex and dynamic systems exhibiting both spatial and temporal heterogeneity. They are influenced by various environmental factors and by host-parasite and inter-parasite interactions. We expect that the described methodology facilitates ecological and biodiversity research of diplostomid parasites. It is also adaptable to other parasite groups where it could serve to improve current understanding of diversity, distribution, and interspecies interactions of other understudied taxa.
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Affiliation(s)
- Alfonso Diaz-Suarez
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia.
| | - Kristina Noreikiene
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia. https://twitter.com/snaudale
| | - Siim Kahar
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - Mikhail Y Ozerov
- Biodiversity Unit, University of Turku, 20014 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland; Department of Aquatic Resources, Swedish University of Agricultural Sciences, Stångholmsvägen 2, 17893 Drottningholm, Sweden
| | - Riho Gross
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Anti Vasemägi
- Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 46, 51006 Tartu, Estonia; Department of Aquatic Resources, Swedish University of Agricultural Sciences, Stångholmsvägen 2, 17893 Drottningholm, Sweden
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36
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Orbay-Cerrato ME, Nilsen RA, Gottdenker N, McManamon R, Elbert JA, Stilwell JM, Ard MB, Ritchie BW, McHale B. Detection of skunk adenovirus-1 in domestic ferrets ( Mustela putorius). Vet Pathol 2024; 61:135-139. [PMID: 37545123 DOI: 10.1177/03009858231189722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
We describe gross pathology, histopathology, ultrastructure, and molecular characterization of skunk adenovirus 1 (SkAdV-1) in 3 ferrets (Mustela putorius) submitted to the Infectious Diseases Laboratory, Zoo and Exotic Animal Pathology Service at the University of Georgia. Case 1 came from a cohort with a 6-week history of multiple ferrets with respiratory disease and mortality. Cases 2 and 3 were submitted 19 days later; they died 3 days after arrival at the vendor's facility. Histopathological evaluation found evidence of suppurative bronchopneumonia, with intralesional gram-positive cocci in case 1. The others had evidence of subacute multifocal histiocytic and lymphoplasmacytic interstitial pneumonia. Viral isolation, polymerase chain reaction (PCR), and DNA sequencing identified SkAdV-1 in lung tissue. In situ hybridization confirmed adenovirus within the lung lesion, and adenovirus particles were visible under an electron microscope. This is the seventh species in which SkAdV-1 has been identified. Cross-species transmission events have important implications for wildlife management and multispecies facilities.
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Affiliation(s)
| | - Roger Alan Nilsen
- Infectious Diseases Laboratory, University of Georgia, Athens, GA
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Nicole Gottdenker
- Zoo and Exotic Animal Pathology Service, Infectious Diseases Laboratory and the Department of Pathology, University of Georgia, Athens, GA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
- Center for the Ecology of Infectious Diseases, Odum School of Ecology, University of Georgia, Athens, GA
| | - Rita McManamon
- Infectious Diseases Laboratory, University of Georgia, Athens, GA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Jessica A Elbert
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Justin M Stilwell
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS
| | - Mary B Ard
- Georgia Electron Microscopy, Office of Research, University of Georgia, Athens, GA
| | - Branson W Ritchie
- Infectious Diseases Laboratory, University of Georgia, Athens, GA
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA
- Zoo and Exotic Animal Pathology Service, Infectious Diseases Laboratory and the Department of Pathology, University of Georgia, Athens, GA
| | - Brittany McHale
- Infectious Diseases Laboratory, University of Georgia, Athens, GA
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA
- Zoo and Exotic Animal Pathology Service, Infectious Diseases Laboratory and the Department of Pathology, University of Georgia, Athens, GA
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Wang Y, Sharma A, Weber KM, Topper E, Appleton AA, Gustafson D, Clish CB, Kaplan RC, Burk RD, Qi Q, Peters BA. The menopause-related gut microbiome: associations with metabolomics, inflammatory protein markers, and cardiometabolic health in women with HIV. Menopause 2024; 31:52-64. [PMID: 38086007 PMCID: PMC10841550 DOI: 10.1097/gme.0000000000002287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
OBJECTIVE This study aimed to identify menopause-related gut microbial features, as well as their related metabolites and inflammatory protein markers, and link with cardiometabolic risk factors in women with and without HIV. METHODS In the Women's Interagency HIV Study, we performed shotgun metagenomic sequencing on 696 stool samples from 446 participants (67% women with HIV), and quantified plasma metabolomics and serum proteomics in a subset (~86%). We examined the associations of menopause (postmenopausal vs premenopausal) with gut microbial features in a cross-sectional repeated-measures design and further evaluated those features in relation to metabolites, proteins, and cardiometabolic risk factors. RESULTS Different overall gut microbial composition was observed by menopausal status in women with HIV only. We identified a range of gut microbial features that differed between postmenopausal and premenopausal women with HIV (but none in women without HIV), including abundance of 32 species and functional potentials involving 24 enzymatic reactions and lower β-glucuronidase bacterial gene ortholog. Specifically, highly abundant species Faecalibacterium prausnitzii , Bacteroides species CAG:98 , and Bifidobacterium adolescentis were depleted in postmenopausal versus premenopausal women with HIV. Menopause-depleted species (mainly Clostridia ) in women with HIV were positively associated with several glycerophospholipids, while negatively associated with imidazolepropionic acid and fibroblast growth factor 21. Mediation analysis suggested that menopause may decrease plasma phosphatidylcholine plasmalogen C36:1 and C36:2 levels via reducing abundance of species F. prausnitzii and Acetanaerobacterium elongatum in women with HIV. Furthermore, waist-to-hip ratio was associated with menopause-related microbes, metabolites, and fibroblast growth factor 21 in women with HIV. CONCLUSIONS Menopause was associated with a differential gut microbiome in women with HIV, related to metabolite and protein profiles that potentially contribute to elevated cardiometabolic risk.
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Affiliation(s)
- Yi Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Elizabeth Topper
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Allison A. Appleton
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, NY, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A. Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
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De Franco E, Owens NDL, Montaser H, Wakeling MN, Saarimäki-Vire J, Triantou A, Ibrahim H, Balboa D, Caswell RC, Jennings RE, Kvist JA, Johnson MB, Muralidharan S, Ellard S, Wright CF, Maddirevula S, Alkuraya FS, Hanley NA, Flanagan SE, Otonkoski T, Hattersley AT, Imbeault M. Primate-specific ZNF808 is essential for pancreatic development in humans. Nat Genet 2023; 55:2075-2081. [PMID: 37973953 PMCID: PMC10703691 DOI: 10.1038/s41588-023-01565-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
Abstract
Identifying genes linked to extreme phenotypes in humans has the potential to highlight biological processes not shared with all other mammals. Here, we report the identification of homozygous loss-of-function variants in the primate-specific gene ZNF808 as a cause of pancreatic agenesis. ZNF808 is a member of the KRAB zinc finger protein family, a large and rapidly evolving group of epigenetic silencers which target transposable elements. We show that loss of ZNF808 in vitro results in aberrant activation of regulatory potential contained in the primate-specific transposable elements it represses during early pancreas development. This leads to inappropriate specification of cell fate with induction of genes associated with liver identity. Our results highlight the essential role of ZNF808 in pancreatic development in humans and the contribution of primate-specific regions of the human genome to congenital developmental disease.
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Affiliation(s)
- Elisa De Franco
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK
| | - Nick D L Owens
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK
| | - Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew N Wakeling
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Athina Triantou
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Diego Balboa
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Richard C Caswell
- Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Rachel E Jennings
- Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jouni A Kvist
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew B Johnson
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK
| | - Sachin Muralidharan
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sian Ellard
- Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Caroline F Wright
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Neil A Hanley
- Division of Diabetes, Endocrinology & Gastroenterology, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
- Endocrinology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sarah E Flanagan
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland.
| | - Andrew T Hattersley
- Institute of Clinical and Biomedical Sciences, University of Exeter Faculty of Health and Life Sciences, Exeter, UK.
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Pérez-Umphrey AA, Settlecowski AE, Elbers JP, Williams ST, Jonsson CB, Bonisoli-Alquati A, Snider AM, Taylor SS. Genetic variants associated with hantavirus infection in a reservoir host are related to regulation of inflammation and immune surveillance. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105525. [PMID: 37956745 DOI: 10.1016/j.meegid.2023.105525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/14/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023]
Abstract
The immunogenetics of wildlife populations influence the epidemiology and evolutionary dynamic of the host-pathogen system. Profiling immune gene diversity present in wildlife may be especially important for those species that, while not at risk of disease or extinction themselves, are host to diseases that are a threat to humans, other wildlife, or livestock. Hantaviruses (genus: Orthohantavirus) are globally distributed zoonotic RNA viruses with pathogenic strains carried by a diverse group of rodent hosts. The marsh rice rat (Oryzomys palustris) is the reservoir host of Orthohantavirus bayoui, a hantavirus that causes fatal cases of hantavirus cardiopulmonary syndrome in humans. We performed a genome wide association study (GWAS) using the rice rat "immunome" (i.e., all exons related to the immune response) to identify genetic variants associated with infection status in wild-caught rice rats naturally infected with their endemic strain of hantavirus. First, we created an annotated reference genome using 10× Chromium Linked Reads sequencing technology. This reference genome was used to create custom baits which were then used to target enrich prepared rice rat libraries (n = 128) and isolate their immunomes prior to sequencing. Top SNPs in the association test were present in four genes (Socs5, Eprs, Mrc1, and Il1f8) which have not been previously implicated in hantavirus infections. However, these genes correspond with other loci or pathways with established importance in hantavirus susceptibility or infection tolerance in reservoir hosts: the JAK/STAT, MHC, and NFκB. These results serve as informative markers for future exploration and highlight the importance of immune pathways that repeatedly emerge across hantavirus systems. Our work aids in creating cross-species comparisons for better understanding mechanisms of genetic susceptibility and host-pathogen coevolution in hantavirus systems.
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Affiliation(s)
- Anna A Pérez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA.
| | - Amie E Settlecowski
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Jean P Elbers
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - S Tyler Williams
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, University of Tennessee Health Science Center, University of Tennessee, 858 Madison Ave., Memphis, TN 38163, USA
| | - Andrea Bonisoli-Alquati
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA; Department of Biological Sciences, California State Polytechnic University-Pomona, Pomona, CA 91768, USA
| | - Allison M Snider
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA
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Glass JR, Harrington RC, Cowman PF, Faircloth BC, Near TJ. Widespread sympatry in a species-rich clade of marine fishes (Carangoidei). Proc Biol Sci 2023; 290:20230657. [PMID: 37909084 PMCID: PMC10618865 DOI: 10.1098/rspb.2023.0657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023] Open
Abstract
A universal paradigm describing patterns of speciation across the tree of life has been debated for decades. In marine organisms, inferring patterns of speciation using contemporary and historical patterns of biogeography is challenging due to the deficiency of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species' dispersal, range size and co-occurrence. Most research on global patterns of marine fish speciation and biogeography has focused on coral reef or pelagic species. Carangoidei is an ecologically important clade of marine fishes that use coral reef and pelagic environments. We used sequence capture of 1314 ultraconserved elements (UCEs) from 154 taxa to generate a time-calibrated phylogeny of Carangoidei and its parent clade, Carangiformes. Age-range correlation analyses of the geographical distributions and divergence times of sister species pairs reveal widespread sympatry, with 73% of sister species pairs exhibiting sympatric geographical distributions, regardless of node age. Most species pairs coexist across large portions of their ranges. We also observe greater disparity in body length and maximum depth between sympatric relative to allopatric sister species. These and other ecological or behavioural attributes probably facilitate sympatry among the most closely related carangoids.
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Affiliation(s)
- Jessica R. Glass
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Richard C. Harrington
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Peter F. Cowman
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland 4810, Australia
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Yale Peabody Museum of Natural History, Division of Vertebrate Zoology. New Haven, CT 06520, USA
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Reichard M, Koblmüller S, Blažek R, Zimmermann H, Katongo C, Bryjová A, Bryja J. Lack of host specialization despite selective host use in brood parasitic cuckoo catfish. Mol Ecol 2023; 32:6070-6082. [PMID: 37861460 DOI: 10.1111/mec.17173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Host-parasite dynamics involve coevolutionary arms races, which may lead to host specialization and ensuing diversification. Our general understanding of the evolution of host specialization in brood parasites is compromised by a restricted focus on bird and insect lineages. The cuckoo catfish (Synodontis multipunctatus) is an obligate parasite of parental care of mouthbrooding cichlids in Lake Tanganyika. Given the ecological and taxonomic diversity of mouthbrooding cichlids in the lake, we hypothesized the existence of sympatric host-specific lineages in the cuckoo catfish. In a sample of 779 broods from 20 cichlid species, we found four species parasitized by cuckoo catfish (with prevalence of parasitism of 2%-18%). All parasitized cichlids were from the tribe Tropheini, maternal mouthbrooders that spawn over a substrate (rather than in open water). Phylogenetic analysis based on genomic (ddRAD sequencing) and mitochondrial (Dloop) data from cuckoo catfish embryos showed an absence of host-specific lineages. This was corroborated by analyses of genetic structure and co-ancestry matrix. Within host species, parasitism was not associated with any individual characteristic we recorded (parent size, water depth), but was costly as parasitized parents carried smaller clutches of their own offspring. We conclude that the cuckoo catfish is an intermediate generalist and discuss costs, benefits and constraints of host specialization in this species and brood parasites in general.
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Affiliation(s)
- Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Radim Blažek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Holger Zimmermann
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Biology, University of Graz, Graz, Austria
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Anna Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Morrissey D, Gordon JD, Saso E, Bilewitch JP, Taylor ML, Hayes V, McFadden CS, Quattrini AM, Allcock AL. Bamboozled! Resolving deep evolutionary nodes within the phylogeny of bamboo corals (Octocorallia: Scleralcyonacea: Keratoisididae). Mol Phylogenet Evol 2023; 188:107910. [PMID: 37640170 DOI: 10.1016/j.ympev.2023.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/22/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups - D1 and D2, and A1 and M1 - needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters.
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Affiliation(s)
- Declan Morrissey
- Ryan Institute & School of Natural Sciences, University of Galway, University Road, Galway, Ireland.
| | - Jessica D Gordon
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Emma Saso
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), 301 Evans Bay Parade, Wellington 6021, New Zealand
| | - Michelle L Taylor
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Vonda Hayes
- Department of Fisheries and Oceans, St. John's, Newfoundland and Labrador, Canada
| | - Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711, USA
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - A Louise Allcock
- Ryan Institute & School of Natural Sciences, University of Galway, University Road, Galway, Ireland
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Baldwin E, McNair M, Leebens-Mack J. Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny. FRONTIERS IN PLANT SCIENCE 2023; 14:1237749. [PMID: 37711293 PMCID: PMC10497973 DOI: 10.3389/fpls.2023.1237749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023]
Abstract
Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genus Sarracenia L. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis of Sarracenia estimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring in Sarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembled de-novo from sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history of Sarracenia.
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Affiliation(s)
- Ethan Baldwin
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Mason McNair
- Department of Plant & Environmental Science, Clemson University, Florence, SC, United States
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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Oksanen S, Saarinen R, Korkiakoski A, Lamminmäki U, Huovinen T. Genotyped functional screening of soluble Fab clones enables in-depth analysis of mutation effects. Sci Rep 2023; 13:13107. [PMID: 37567990 PMCID: PMC10421887 DOI: 10.1038/s41598-023-40241-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) and their fragments are widely used in therapeutics, diagnostics and basic research. Although display methods such as phage display offer high-throughput, affinities of individual antibodies need to be accurately measured in soluble format. We have developed a screening platform capable of providing genotyped functional data from a total of 9216 soluble, individual antigen binding fragment (Fab) clones by employing next-generation sequencing (NGS) with hierarchical indexing. Full-length, paired variable domain sequences (VL-VH) are linked to functional screening data, enabling in-depth analysis of mutation effects. The platform was applied to four phage display-selected scFv/Fab screening projects and one site-saturation VH affinity maturation project. Genotyped functional screening simultaneously enabled the identification of affinity improving mutations in the VH domain of Fab 49A3 recognizing Dengue virus non-structural protein 1 (NS1) serotype 2 and informed on VH residue positions which cannot be changed from wild-type without decreasing the affinity. Genotype-based identification revealed to us the extent of intraclonal signal variance inherent to single point screening data, a phenomenon often overlooked in the field. Moreover, genotyped screening eliminated the redundant selection of identical genotypes for further study and provided a new analysis tool to evaluate the success of phage display selections and remaining clonal diversity in the screened repertoires.
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Affiliation(s)
- Sami Oksanen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
| | - Roope Saarinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | | | - Urpo Lamminmäki
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
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McCormack JE, Hill MM, DeRaad DA, Kirsch EJ, Reckling KR, Mutchler MJ, Ramirez BR, Campbell RML, Salter JF, Pizarro AK, Tsai WLE, Bonaccorso E. An elevational shift facilitated the Mesoamerican diversification of Azure-hooded Jays ( Cyanolyca cucullata) during the Great American Biotic Interchange. Ecol Evol 2023; 13:e10411. [PMID: 37589041 PMCID: PMC10425738 DOI: 10.1002/ece3.10411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/18/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023] Open
Abstract
The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time-calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre-land bridge dispersal from Mesoamerica to South America 6.3-7.3 Mya, followed by a back-colonization of C. cucullata to Mesoamerica 2.3-4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata. This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time-calibrated phylogeny suggests was already populated by higher-elevation, congeneric dwarf-jays (C. argentigula, C. pumilo, C. mirabilis, and C. nanus). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrata and C. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern-day species assemblages in the Americas.
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Affiliation(s)
- John E. McCormack
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Molly M. Hill
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Devon A. DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansasUSA
| | - Eliza J. Kirsch
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | | | - Brenda R. Ramirez
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | - Jessie F. Salter
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCaliforniaUSA
| | - Alana K. Pizarro
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | | | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de QuitoQuitoEcuador
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Settlecowski AE, Marks BD, Manthey JD. Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens. Ecol Evol 2023; 13:e10407. [PMID: 37565027 PMCID: PMC10410627 DOI: 10.1002/ece3.10407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/28/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high-throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA sources. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low-coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: (1) double-stranded DNA (dsDNA), single tube (KAPA); (2) single-stranded DNA (ssDNA), multi-tube (IDT); and (3) ssDNA, single tube (Claret Bioscience). We found that the ssDNA, multi-tube method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best-performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.
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Affiliation(s)
- Amie E. Settlecowski
- Bird Collection Gantz Family Collections CenterThe Field MuseumChicagoIllinoisUSA
| | - Ben D. Marks
- Bird Collection Gantz Family Collections CenterThe Field MuseumChicagoIllinoisUSA
| | - Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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Talavera A, Nie ZL, Ma ZY, Johnson G, Ickert-Bond SM, Zimmer EA, Wen J. Phylogenomic analyses using a new 1013-gene Vitaceae bait-set support major groups of North American Vitis. Mol Phylogenet Evol 2023:107866. [PMID: 37354923 DOI: 10.1016/j.ympev.2023.107866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
A set of newly designed Vitaceae baits targeting 1013 genes was employed to explore phylogenetic relationships among North American Vitis. Eurasian Vitis taxa including Vitis vinifera were found to be nested within North American Vitis subgenus Vitis. North American Vitis subgenus Vitis can be placed into nine main groups: the Monticola group, the Occidentales group, the Californica group, the Vinifera group (introduced from Eurasia), the Mustangensis group, the Palmata group, the Aestivalis group, the Labrusca group, and the Cinerea group. Strong cytonuclear discordances were detected in North American Vitis, with many species non-monophyletic in the plastid phylogeny, while monophyletic in the nuclear phylogeny. The phylogenomic analyses support recognizing four distinct species in the Vitis cinerea complex in North America: V. cinerea, V. baileyana, V. berlandieri, and V. simpsonii. Such treatment will better serve the conservation of wild Vitis diversity in North America. Yet the evolutionary history of Vitis is highly complex, with the concordance analyses indicating conflicting signals across the phylogeny. Cytonuclear discordances and Analyses using the Species Networks applying Quartets (SNaQ) method support extensive hybridizations in North American Vitis. The results further indicate that plastid genomes alone are insufficient for resolving the evolutionary history of plant groups that have undergone rampant hybridization, like the case in North American Vitis. Nuclear gene data are essential for species delimitation, identification and reconstructing evolutionary relationships; therefore, they are imperative for plant phylogenomic studies.
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Affiliation(s)
- Alicia Talavera
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA; Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, 29071, Málaga, Spain.
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China
| | - Zhi-Yao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518000 China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Stefanie M Ickert-Bond
- UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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Frederick JC, Thompson AT, Sharma P, Dharmarajan G, Ronai I, Pesapane R, Smith RC, Sundstrom KD, Tsao JI, Tuten HC, Yabsley MJ, Glenn TC. Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity. Mol Ecol 2023; 32:3133-3149. [PMID: 36912202 DOI: 10.1111/mec.16921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
The blacklegged tick (Ixodes scapularis (Journal of the Academy of Natural Sciences of Philadelphia, 1821, 2, 59)) is a vector of Borrelia burgdorferi sensu stricto (s.s.) (International Journal of Systematic Bacteriology, 1984, 34, 496), the causative bacterial agent of Lyme disease, part of a slow-moving epidemic of Lyme borreliosis spreading across the northern hemisphere. Well-known geographical differences in the vectorial capacity of these ticks are associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographical studies of these ticks have been restricted to relatively few populations or few genetic loci. Here we present the most comprehensive phylogeographical study of genome-wide markers in I. scapularis, conducted by using 3RAD (triple-enzyme restriction-site associated sequencing) and surveying 353 ticks from 33 counties throughout the species' range. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify five spatially associated genetic clusters of I. scapularis. In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme-endemic regions. Finally, we identify 10 variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome-scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis.
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Affiliation(s)
- Julia C Frederick
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, 30602, USA
| | - Alec T Thompson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
- Center for the Ecology of Infectious Diseases, Odom School of Ecology, University of Georgia, Athens, Georgia, 30602, USA
| | - Prisha Sharma
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, 30602, USA
| | - Guha Dharmarajan
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, 29808, USA
- Division of Sciences, School of Interwoven Arts and Sciences, Krea University, Sri City, Andhra Pradesh, India
| | - Isobel Ronai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Risa Pesapane
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Ryan C Smith
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa, 50011, USA
| | - Kellee D Sundstrom
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Jean I Tsao
- Department of Wildlife and Fisheries, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Holly C Tuten
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, Illinois, 61820, USA
| | - Michael J Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
- Center for the Ecology of Infectious Diseases, Odom School of Ecology, University of Georgia, Athens, Georgia, 30602, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA
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49
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Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
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50
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Wang Z, Peters BA, Bryant M, Hanna DB, Schwartz T, Wang T, Sollecito CC, Usyk M, Grassi E, Wiek F, Peter LS, Post WS, Landay AL, Hodis HN, Weber KM, French A, Golub ET, Lazar J, Gustafson D, Sharma A, Anastos K, Clish CB, Burk RD, Kaplan RC, Knight R, Qi Q. Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection. MICROBIOME 2023; 11:119. [PMID: 37237391 PMCID: PMC10224225 DOI: 10.1186/s40168-023-01566-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Alterations in gut microbiota have been implicated in HIV infection and cardiovascular disease. However, how gut microbial alterations relate to host inflammation and metabolite profiles, and their relationships with atherosclerosis, have not been well-studied, especially in the context of HIV infection. Here, we examined associations of gut microbial species and functional components measured by shotgun metagenomics with carotid artery plaque assessed by B-mode carotid artery ultrasound in 320 women with or at high risk of HIV (65% HIV +) from the Women's Interagency HIV Study. We further integrated plaque-associated microbial features with serum proteomics (74 inflammatory markers measured by the proximity extension assay) and plasma metabolomics (378 metabolites measured by liquid chromatography tandem mass spectrometry) in relation to carotid artery plaque in up to 433 women. RESULTS Fusobacterium nucleatum, a potentially pathogenic bacteria, was positively associated with carotid artery plaque, while five microbial species (Roseburia hominis, Roseburia inulinivorans, Johnsonella ignava, Odoribacter splanchnicus, Clostridium saccharolyticum) were inversely associated with plaque. Results were consistent between women with and without HIV. Fusobacterium nucleatum was positively associated with several serum proteomic inflammatory markers (e.g., CXCL9), and the other plaque-related species were inversely associated with proteomic inflammatory markers (e.g., CX3CL1). These microbial-associated proteomic inflammatory markers were also positively associated with plaque. Associations between bacterial species (especially Fusobacterium nucleatum) and plaque were attenuated after further adjustment for proteomic inflammatory markers. Plaque-associated species were correlated with several plasma metabolites, including the microbial metabolite imidazole-propionate (ImP), which was positively associated with plaque and several pro-inflammatory markers. Further analysis identified additional bacterial species and bacterial hutH gene (encoding enzyme histidine ammonia-lyase in ImP production) associated with plasma ImP levels. A gut microbiota score based on these ImP-associated species was positively associated with plaque and several pro-inflammatory markers. CONCLUSION Among women living with or at risk of HIV, we identified several gut bacterial species and a microbial metabolite ImP associated with carotid artery atherosclerosis, which might be related to host immune activation and inflammation. Video Abstract.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Evan Grassi
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Fanua Wiek
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lauren St Peter
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wendy S Post
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Howard N Hodis
- Atherosclerosis Research Unit, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Audrey French
- Department of Internal Medicine, Stroger Hospital of Cook County, Chicago, IL, USA
| | - Elizabeth T Golub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jason Lazar
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kathryn Anastos
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
- Department of Bioengineering, University of California, La Jolla, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California, La Jolla, San Diego, CA, USA
- Center for Microbiome Innovation, University of California, La Jolla, San Diego, CA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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