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  • 1
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    Curatorial guidelines and standards of the American Society of Mammalogists for collections of genetic resources
    Oxford University Press (OUP) ; 2019
    In:  Journal of Mammalogy Vol. 100, No. 5 ( 2019-10-22), p. 1690-1694
    Details
    In: Journal of Mammalogy, Oxford University Press (OUP), Vol. 100, No. 5 ( 2019-10-22), p. 1690-1694
    Abstract: The Systematic Collections Committee of the American Society of Mammalogists advises curators and other personnel affiliated with natural history collections in matters relating to administration, curation, and accreditation of mammal specimens and their associated data. The Systematic Collections Committee also maintains a list of curatorial standards for managing a collection-accreditation program under the auspices of the American Society of Mammalogists. To date, the Systematic Collections Committee has provided guidance for the more traditional specimen collections (skin, skeletal, fluid, etc.) and specimen data management. Given the rapidly expanding role of genetic resources in biological research, the Systematic Collections Committee herein presents a series of formal guidelines and standards designed to assist collections professionals in the current best practices for curation and maintenance of collections of genetic resources, to ensure long-term integrity of the archived material, and to address personnel safety and guidelines for researchers and curatorial staff. These guidelines and standards are intended to provide constructive guidance and a mechanism of accreditation for collections that vary in scale and infrastructure. El Comité de Colecciones Sistemáticas de la Sociedad Americana de Mastozoólogos asesora a curadores y demás personal afiliado a colecciones de historia natural en asuntos relacionados a la administración, curación y acreditación de especímenes de mamíferos y su información pertinente. El Comité de Colecciones Sistemáticas mantiene también una lista de normas curatoriales para la gestión de un programa de acreditación de colecciones auspiciados por la Sociedad Americana de Mastozoólogos. A la fecha, el Comité de Colecciones Sistemáticas ha proporcionado una guía para las colecciones de muestras tradicionales (piel, esqueleto, líquido, etc.) y el manejo de datos asociados a estos especímenes. Dado el rápido crecimiento del papel que desempeñan los recursos genéticos en investigaciones biológicas, el Comité de Colecciones Sistemáticas presenta en esta publicación una serie de pautas y estándares formales diseñados para ayudar a los profesionales de colecciones científicas en las mejores prácticas actuales para la conservación y mantenimiento de colecciones de recursos genéticos, a modo de garantizar la integridad a largo plazo del material archivado, y tratar sobre la seguridad del personal y directrices para investigadores y personal curatorial. Estas pautas y estándares tienen como objetivo proporcionar una orientación constructiva y un mecanismo de acreditación para colecciones que varían en escala e infraestructura.
    Type of Medium: Online Resource
    ISSN: 0022-2372 , 1545-1542
    URL: Article
    DOI: 10.1093/jmammal/gyz111
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2066602-0
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  • 2
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    Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
    Springer Science and Business Media LLC ; 2022
    In:  Nature Microbiology Vol. 7, No. 12 ( 2022-11-28), p. 2128-2150
    Details
    In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 7, No. 12 ( 2022-11-28), p. 2128-2150
    Abstract: Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
    Type of Medium: Online Resource
    ISSN: 2058-5276
    URL: Article
    DOI: 10.1038/s41564-022-01266-x
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2845610-5
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  • 3
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    Cohort-based learning for microbiome research community standards
    Springer Science and Business Media LLC ; 2023
    In:  Nature Microbiology Vol. 8, No. 5 ( 2023-04-17), p. 751-753
    Details
    In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 8, No. 5 ( 2023-04-17), p. 751-753
    Type of Medium: Online Resource
    ISSN: 2058-5276
    URL: Article
    DOI: 10.1038/s41564-023-01361-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2845610-5
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  • 4
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    Avian host composition, local speciation and dispersal drive the regional assembly of avian malaria parasites in South American birds
    Wiley ; 2019
    In:  Molecular Ecology Vol. 28, No. 10 ( 2019-05), p. 2681-2693
    Details
    In: Molecular Ecology, Wiley, Vol. 28, No. 10 ( 2019-05), p. 2681-2693
    Abstract: Identifying the ecological factors that shape parasite distributions remains a central goal in disease ecology. These factors include dispersal capability, environmental filters and geographic distance. Using 520 haemosporidian parasite genetic lineages recovered from 7,534 birds sampled across tropical and temperate South America, we tested (a) the latitudinal diversity gradient hypothesis and (b) the distance–decay relationship (decreasing proportion of shared species between communities with increasing geographic distance) for this host–parasite system. We then inferred the biogeographic processes influencing the diversity and distributions of this cosmopolitan group of parasites across South America. We found support for a latitudinal gradient in diversity for avian haemosporidian parasites, potentially mediated through higher avian host diversity towards the equator. Parasite similarity was correlated with climate similarity, geographic distance and host composition. Local diversification in Amazonian lineages followed by dispersal was the most frequent biogeographic events reconstructed for haemosporidian parasites. Combining macroecological patterns and biogeographic processes, our study reveals that haemosporidian parasites are capable of circumventing geographic barriers and dispersing across biomes, although constrained by environmental filtering. The contemporary diversity and distributions of haemosporidian parasites are mainly driven by historical (speciation) and ecological (dispersal) processes, whereas the parasite community assembly is largely governed by host composition and to a lesser extent by environmental conditions.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2019.28.issue-10
    DOI: 10.1111/mec.15094
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 5
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    Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network
    Public Library of Science (PLoS) ; 2021
    In:  PLOS Pathogens Vol. 17, No. 6 ( 2021-6-3), p. e1009583-
    Details
    In: PLOS Pathogens, Public Library of Science (PLoS), Vol. 17, No. 6 ( 2021-6-3), p. e1009583-
    Abstract: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.
    Type of Medium: Online Resource
    ISSN: 1553-7374
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.1371/journal.ppat.1009583
    DOI: 10.1371/journal.ppat.1009583.g001
    DOI: 10.1371/journal.ppat.1009583.g002
    DOI: 10.1371/journal.ppat.1009583.g003
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2021
    detail.hit.zdb_id: 2205412-1
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  • 6
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    A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis
    American Society for Microbiology ; 2019
    In:  mSystems Vol. 4, No. 4 ( 2019-08-27)
    Details
    In: mSystems, American Society for Microbiology, Vol. 4, No. 4 ( 2019-08-27)
    Abstract: The European common cuttlefish, Sepia officinalis , is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae . The esophagus was dominated by a single ASV of the genus Vibrio . Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family Piscirickettsiaceae , which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity and that the esophagus and gills are major colonization sites. IMPORTANCE Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio ( Aliivibrio ) fischeri in the light organ of the bobtail squid and the role of Alpha - and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio , as well as colonization of gills by Piscirickettsiaceae . This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/mSystems.00177-19
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
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  • 7
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    Body Size Poorly Predicts Host-Associated Microbial Diversity in Wild Birds
    American Society for Microbiology ; 2023
    In:  Microbiology Spectrum Vol. 11, No. 3 ( 2023-06-15)
    Details
    In: Microbiology Spectrum, American Society for Microbiology, Vol. 11, No. 3 ( 2023-06-15)
    Abstract: The composition and diversity of avian microbiota are shaped by many factors, including host ecologies and environmental variables. In this study, we examine microbial diversity across 214 bird species sampled in Malawi at five major body sites: blood, buccal cavity, gizzard, intestinal tract, and cloaca. Microbial community dissimilarity differed significantly across body sites. Ecological theory predicts that as area increases, so does diversity. We tested the hypothesis that avian microbiota diversity is correlated with body size, used as a proxy for area, using comparative phylogenetic methods. Using Pagel’s lambda, we found that few microbial diversity metrics had significant phylogenetic signals. Phylogenetic generalized least squares identified a significant but weak negative correlation between host size and microbial diversity of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host size among birds within the order Passeriformes . Phylosymbiosis, or a congruent branching pattern between host phylogeny and their associated microbiota similarity, was tested and found to be weak or not significant in four of the body sites with sufficient sample size (blood, buccal, cloaca, and intestines). Taken together, these results suggest that the avian microbiome is highly variable, with microbiota diversity demonstrating few clear associations with bird size. Finally, the blood microbiota have a unique relationship with host size. IMPORTANCE All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms. However, the general rules that govern these host-associated microbial communities are poorly described, especially in wild animals. In this paper, we investigate the microbial communities of over 200 species of birds from Malawi and characterize five body site bacterial microbiota in depth. Because the evolutionary relationships of the host underlie the relationship between any host-associated microbiota relationships, we use phylogenetic comparative methods to account for this relationship. We find that the size of a host (the bird) and the diversity and composition of the microbiota are largely uncorrelated. We also find that the general pattern of similarity between host phylogeny and microbiota similarity is weak. Together, we see that bird microbiota are not strongly tied to host size or evolutionary history.
    Type of Medium: Online Resource
    ISSN: 2165-0497
    URL: Article
    DOI: 10.1128/spectrum.03749-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2807133-5
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  • 8
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    Building Natural History Collections for the Twenty-First Century and Beyond
    Oxford University Press (OUP) ; 2020
    In:  BioScience Vol. 70, No. 8 ( 2020-08-01), p. 674-687
    Details
    In: BioScience, Oxford University Press (OUP), Vol. 70, No. 8 ( 2020-08-01), p. 674-687
    Abstract: Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.
    Type of Medium: Online Resource
    ISSN: 0006-3568 , 1525-3244
    URL: Article
    DOI: 10.1093/biosci/biaa069
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2066019-4
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  • 9
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    Juvenile Hormone-Sensitive Ribosomal Activity Enhances Viral Replication in Aedes aegypti
    American Society for Microbiology ; 2021
    In:  mSystems Vol. 6, No. 3 ( 2021-06-29)
    Details
    In: mSystems, American Society for Microbiology, Vol. 6, No. 3 ( 2021-06-29)
    Abstract: Zika virus (ZIKV; Flaviviridae ) is a devastating virus transmitted to humans by the mosquito Aedes aegypti . The interaction of the virus with the mosquito vector is poorly known. The double-stranded RNA (dsRNA)-mediated interruption or activation of immunity-related genes in the Toll, IMD, JAK-STAT, and short interfering RNA (siRNA) pathways did not affect ZIKV infection in A. aegypti . Transcriptome-based analysis indicated that most immunity-related genes were upregulated in response to ZIKV infection, including leucine-rich immune protein (LRIM) genes. Further, there was a significant increment in the ZIKV load in LRIM9- , LRIM10A- , and LIRM10B -silenced A. aegypti , suggesting their function in modulating viral infection. Further, gene function enrichment analysis revealed that viral infection increased global ribosomal activity. Silencing of RpL23 and RpL27 , two ribosomal large subunit genes, increased mosquito resistance to ZIKV infection. In vitro fat body culture assay revealed that the expression of RpL23 and RpL27 was responsive to the Juvenile hormone (JH) signaling pathway. These two genes were transcriptionally regulated by JH and its receptor methoprene-tolerant (Met) complex. Silencing of Met also inhibited ZIKV infection in A. aegypti . This suggests that ZIKV enhances ribosomal activity through JH regulation to promote infection in mosquitoes. Together, these data reveal A. aegypti immune responses to ZIKV and suggest a control strategy that reduces ZIKV transmission by modulating host factors. IMPORTANCE Most flaviviruses are transmitted between hosts by arthropod vectors such as mosquitoes. Since therapeutics or vaccines are lacking for most mosquito-borne diseases, reducing the mosquito vector competence is an effective way to decrease disease burden. We used high-throughput sequencing technology to study the interaction between mosquito Aedes aegypti and ZIKV. Leucine-rich immune protein (LRIM) genes were involved in the defense in response to viral infection. In addition, RNA interference (RNAi) silencing of RpL23 and RpL27 , two JH-regulated ribosomal large subunit genes, suppressed ZIKV infection in A. aegypti . These results suggest a novel control strategy that could block the transmission of ZIKV.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/mSystems.01190-20
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2844333-0
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  • 10
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    Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor
    American Society for Microbiology ; 2020
    In:  mSystems Vol. 5, No. 6 ( 2020-12-22)
    Details
    In: mSystems, American Society for Microbiology, Vol. 5, No. 6 ( 2020-12-22)
    Abstract: The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associated diplomonads. Furthermore, most of the close relatives within Fornicata are free-living organisms. This leaves the lifestyle of the ancestor unclear. Here, we present metabolic maps of four different diplomonad species. We identified 853 metabolic reactions and 147 pathways present in at least one of the analyzed diplomonads. Our study suggests that diplomonads represent a metabolically diverse group in which differences correlate with different environments (e.g., the detoxification of arsenic). Using a parsimonious analysis, we also provide a description of the putative metabolism of the last Diplomonadida common ancestor. Our results show that the acquisition and loss of reactions have shaped metabolism since this common ancestor. There is a net loss of reaction in all branches leading to parasitic diplomonads, suggesting an ongoing reduction in the metabolic capacity. Important traits present in host-associated diplomonads (e.g., virulence factors and the synthesis of UDP- N- acetyl- d- galactosamine) are shared with free-living relatives. The last Diplomonadida common ancestor most likely already had acquired important enzymes for the salvage of nucleotides and had a reduced capacity to synthesize nucleotides, lipids, and amino acids de novo , suggesting that it was an obligate host-associated organism. IMPORTANCE Diplomonads are a group of microbial eukaryotes found in oxygen-poor environments. There are both parasitic (e.g., Giardia intestinalis ) and free-living (e.g., Trepomonas ) members in the group. Diplomonads are well known for their anaerobic metabolism, which has been studied for many years. Here, we reconstructed whole metabolic networks of four extant diplomonad species as well as their ancestors, using a bioinformatics approach. We show that the metabolism within the group is under constant change throughout evolutionary time, in response to the environments that the different lineages explore. Both gene losses and gains are responsible for the adaptation processes. Interestingly, it appears that the last Diplomonadida common ancestor had a metabolism that is more similar to extant parasitic than free-living diplomonads. This suggests that the host-associated lifestyle of parasitic diplomonads, such as the human parasite G. intestinalis , is an old evolutionary adaptation.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/mSystems.00774-20
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
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