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Grieneisen L, Hays A, Cook E, Blekhman R, Tecot S. Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type. Am J Primatol 2024:e23656. [PMID: 38873762 DOI: 10.1002/ajp.23656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, BC, Canada
| | - Allison Hays
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Erica Cook
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stacey Tecot
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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Toxoplasmosis in Captive Ring-Tailed Lemurs ( Lemur catta). Pathogens 2022; 11:pathogens11101142. [PMID: 36297199 PMCID: PMC9610425 DOI: 10.3390/pathogens11101142] [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: 08/30/2022] [Revised: 09/21/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022] Open
Abstract
Toxoplasma gondii is one of the most common protozoan parasites and is widely present in all warm-blooded animals. Although clinical disease is uncommon, some species, including ring-tailed lemurs (Lemur catta), have been found to develop acute and lethal toxoplasmosis. The aim of this study was to describe the pathologic, immunohistochemical, serological, and molecular findings of an outbreak of fatal toxoplasmosis in three captive ring-tailed lemurs in Central Italy in 2009. The animals died acutely within few days. The necropsy was immediately performed; necrotic lesions in the spleen, liver, and kidney, as well as interstitial pneumonia, were found histologically. All animals had high titers of anti-T. gondii-specific antibodies (1:1280 IgM and 1:640 IgG) according to a modified agglutination test (MAT) and immunohistochemistry showed scattered tachyzoites in the target organs. Diagnosis was confirmed by PCR and clonal type II was identified. In addition, the seven co-habiting lemurs were seronegative. This paper reports the first outbreak of acute disseminated toxoplasmosis in captive ring-tailed lemurs in Italy. These findings confirm the high susceptibility of this endangered species to toxoplasma infection, which may be considered a further threat to captive population viability.
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Palmada-Flores M, Orkin JD, Haase B, Mountcastle J, Bertelsen MF, Fedrigo O, Kuderna LFK, Jarvis ED, Marques-Bonet T. A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience 2022; 11:6562532. [PMID: 35365833 PMCID: PMC8975718 DOI: 10.1093/gigascience/giac026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 02/19/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. RESULTS We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. CONCLUSIONS mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
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Affiliation(s)
- Marc Palmada-Flores
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Joseph D Orkin
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.,Département d'anthropologie, Université de Montréal, Montréal, QC H3T 1N8, Canada
| | - Bettina Haase
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA
| | | | - Mads F Bertelsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C 1870, Denmark.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksber 1870, Denmark
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA
| | - Lukas F K Kuderna
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain
| | - Erich D Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065, USA.,Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksber 1870, Denmark.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Laboratory of Neurogenetics of Language, The Rockefeller University, NY 10065, USA
| | - Tomas Marques-Bonet
- Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona 08003, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelon 08028a, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
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