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Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiol Spectr 2024; 12:e0359023. [PMID: 38451230 DOI: 10.1128/spectrum.03590-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.
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Affiliation(s)
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Augusto AM, Raposeira H, Horta P, Mata VA, Aizpurua O, Alberdi A, Jones G, Razgour O, Santos SAP, Russo D, Rebelo H. Bat diversity boosts ecosystem services: Evidence from pine processionary moth predation. Sci Total Environ 2024; 912:169387. [PMID: 38110100 DOI: 10.1016/j.scitotenv.2023.169387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023]
Abstract
Coniferous forests contribute to the European economy; however, they have experienced a decline since the late 1990s due to an invasive pest known as the pine processionary moth, Thaumetopoea pityocampa. The impacts of this pest are increasingly exacerbated by climate change. Traditional control strategies involving pesticides have had negative effects on public health and the environment. Instead, forest managers seek a more ecological and sustainable approach to management that promotes the natural actions of pest control agents. This study aims to evaluate the role of bats in suppressing pine processionary moths in pine forests and examine how the bat community composition and abundance influence pest consumption. Bats were sampled in the mountainous environment of the Serra da Estrela in central Portugal to collect faecal samples for DNA meta-barcoding analysis. We assessed the relationship between a) bat richness, b) bat relative abundance, c) bat diet richness, and the frequency of pine processionary moth consumption. Our findings indicate that sites with the highest bat species richness and abundance exhibit the highest levels of pine processionary moth consumption. The intensity of pine processionary moth consumption is independent of insect diversity within the site. The highest occurrence of pine processionary moth presence in bat diets is primarily observed in species that forage in cluttered habitats. A typical predator of pine processionary moths among bats is likely to be a forest-dwelling species that specialises in consuming Lepidoptera. These species primarily use short-range echolocation calls, which are relatively inaudible to tympanate moths, suitable for locating prey in cluttered environments, employing a gleaning hunting strategy. Examples include species from the genera Plecotus, Myotis, and Rhinolophus. This study enhances our understanding of the potential pest consumption services provided by bats in pine forests. The insights gained from this research can inform integrated pest management practices in forestry.
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Affiliation(s)
- A M Augusto
- ICS, Instituto de Ciências Sociais, Universidade de Lisboa, Av. Professor Aníbal de Bettencourt, 9, 1600-189 Lisboa, Portugal.
| | - H Raposeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4099-002, Portugal
| | - P Horta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4099-002, Portugal
| | - V A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - O Aizpurua
- Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - A Alberdi
- Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - G Jones
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - O Razgour
- Biosciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, UK
| | - S A P Santos
- Instituto Politécnico de Setúbal, ESTBarreiro, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal; LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - D Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università 100, I-80055 Portici, Napoli, Italy
| | - H Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Instituto Politécnico de Setúbal, ESS, Campus da Estefanilha, Setúbal, Portugal; NBI, Natural Business Intelligence, Régia Douro Park, 5000-033 Andrães, Vila Real, Portugal
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3
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Koziol A, Odriozola I, Leonard A, Eisenhofer R, San José C, Aizpurua O, Alberdi A. Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors. mBio 2023; 14:e0160623. [PMID: 37650630 PMCID: PMC10653949 DOI: 10.1128/mbio.01606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.
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Affiliation(s)
- Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Aoife Leonard
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carlos San José
- Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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4
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Aizpurua O, Blijleven K, Trivedi U, Gilbert MTP, Alberdi A. Unravelling animal-microbiota evolution on a chip. Trends Microbiol 2023; 31:995-1002. [PMID: 37217368 DOI: 10.1016/j.tim.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023]
Abstract
Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. Gut-on-a-chip models provide an innovative approach that expands beyond the potential of conventional microbiome profiling to study how different animals sense and react to microbes by comparing responses of animal intestinal tissue models to different microbial stimuli. This complementary knowledge can contribute to our understanding of how host genetic features facilitate or prevent different microbiomes from being assembled, and in doing so elucidate the role of host-microbiota interactions in animal evolution.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Kees Blijleven
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Urvish Trivedi
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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5
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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6
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Bolt Botnen A, Bjørnsen MB, Alberdi A, Gilbert MTP, Aizpurua O. A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon 2023; 9:e12861. [PMID: 36699263 PMCID: PMC9868478 DOI: 10.1016/j.heliyon.2023.e12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
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Affiliation(s)
- Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Mads Bjørn Bjørnsen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
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7
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Koziol A, Odriozola I, Nyholm L, Leonard A, San José C, Pauperio J, Ferreira C, Hansen AJ, Aizpurua O, Gilbert MTP, Alberdi A. Enriching captivity conditions with natural elements does not prevent the loss of wild‐like gut microbiota but shapes its compositional variation in two small mammals. Microbiologyopen 2022; 11:e1318. [PMCID: PMC9517064 DOI: 10.1002/mbo3.1318] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild‐like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild‐caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a “natural” setup enriched with elements freshly collected from nature and a “laboratory” setup with sterile artificial elements. Through sequencing of the V3–V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula, suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild‐like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.
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Affiliation(s)
- Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Aoife Leonard
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Carlos San José
- Biodonostia Health Research Institute Donostia‐San Sebastian Spain
| | - Joana Pauperio
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Vila do Conde Campus de Vairão Portugal
| | - Clara Ferreira
- Animal Ecology, Institute for Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Anders J. Hansen
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - M. Thomas P. Gilbert
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
- University Museum, Norwegian University of Science and Technology Trondheim Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
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Nyholm L, Odriozola I, Martin Bideguren G, Aizpurua O, Alberdi A. Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish. PeerJ 2022; 10:e12992. [PMID: 35223211 PMCID: PMC8877339 DOI: 10.7717/peerj.12992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/02/2022] [Indexed: 01/11/2023] Open
Abstract
The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
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Affiliation(s)
- Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Garazi Martin Bideguren
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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9
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Puetz LC, Delmont TO, Aizpurua O, Guo C, Zhang G, Katajamaa R, Jensen P, Gilbert MTP. Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication. Adv Genet (Hoboken) 2021; 2:2100018. [PMID: 36619855 PMCID: PMC9744516 DOI: 10.1002/ggn2.202100018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/04/2021] [Indexed: 01/11/2023]
Abstract
Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.
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Affiliation(s)
- Lara C. Puetz
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Tom O. Delmont
- Génomique MétaboliqueGenoscopeInstitut François JacobCEACNRSUniv EvryUniversité Paris‐SaclayEvry91057France
| | - Ostaizka Aizpurua
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Chunxue Guo
- China National GeneBankBGI‐ShenzhenShenzhen518083China
| | - Guojie Zhang
- China National GeneBankBGI‐ShenzhenShenzhen518083China,Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagen2100Denmark,State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming650223China,Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming650223China
| | - Rebecca Katajamaa
- IFM Biology, AVIAN Behaviour Genomics and Physiology GroupLinköping UniversityLinköping58330Sweden
| | - Per Jensen
- IFM Biology, AVIAN Behaviour Genomics and Physiology GroupLinköping UniversityLinköping58330Sweden
| | - M. Thomas P. Gilbert
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark,Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
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Alberdi A, Martin Bideguren G, Aizpurua O. Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis. Sci Rep 2021; 11:22660. [PMID: 34811423 PMCID: PMC8608908 DOI: 10.1038/s41598-021-02015-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022] Open
Abstract
The gut microbiota is recognised as an essential asset for the normal functioning of animal biology. When wild animals are moved into captivity, the modified environmental pressures are expected to rewire the gut microbiota, yet whether this transition follows similar patterns across vertebrates is still unresolved due to the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species. Our analyses yielded no overall pattern of diversity and compositional variation between wild and captive vertebrates, but a heterogeneous landscape of responses, which differed depending on the components of diversity considered. Captive populations showed enrichment patterns of human-associated microorganisms, and the minimal host phylogenetic signal suggests that changes between wild and captive populations are mainly driven by case-specific captivity conditions. Finally, we show that microbiota differences between wild and captive populations can impact evolutionary and ecological inferences that rely on hierarchical clustering-based comparative analyses of gut microbial communities across species.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Garazi Martin Bideguren
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.
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11
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Aizpurua O, Nyholm L, Morris E, Chaverri G, Herrera Montalvo LG, Flores-Martinez JJ, Lin A, Razgour O, Gilbert MTP, Alberdi A. The role of the gut microbiota in the dietary niche expansion of fishing bats. Anim Microbiome 2021; 3:76. [PMID: 34711286 PMCID: PMC8555116 DOI: 10.1186/s42523-021-00137-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet. Results We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish. Conclusions Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00137-w.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| | - Evie Morris
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica, #4000 Alamedas, Golfito, 60701, Costa Rica.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, República de Panamá
| | - L Gerardo Herrera Montalvo
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 21, San Patricio, 48980, Jalisco, Mexico
| | - José Juan Flores-Martinez
- Laboratorio de Sistemas de Información Geográfica, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Orly Razgour
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
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12
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Nyholm L, Koziol A, Marcos S, Botnen AB, Aizpurua O, Gopalakrishnan S, Limborg MT, Gilbert MTP, Alberdi A. Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research. iScience 2020; 23:101414. [PMID: 32777774 PMCID: PMC7416341 DOI: 10.1016/j.isci.2020.101414] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/18/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the implementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.
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Affiliation(s)
- Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark.
| | - Adam Koziol
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Sofia Marcos
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim 7491, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
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13
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Alberdi A, Razgour O, Aizpurua O, Novella-Fernandez R, Aihartza J, Budinski I, Garin I, Ibáñez C, Izagirre E, Rebelo H, Russo D, Vlaschenko A, Zhelyazkova V, Zrnčić V, Gilbert MTP. DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats. Nat Commun 2020; 11:1154. [PMID: 32123172 PMCID: PMC7052159 DOI: 10.1038/s41467-020-14961-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/29/2020] [Indexed: 11/09/2022] Open
Abstract
Inferences of the interactions between species' ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats' hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.
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Affiliation(s)
- Antton Alberdi
- Centre for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Orly Razgour
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.,Biosciences, University of Exeter, Exeter, EX4 4PY, UK
| | - Ostaizka Aizpurua
- Centre for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353, Copenhagen, Denmark
| | | | | | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, 11060, Serbia
| | - Inazio Garin
- University of the Basque Country UPV/EHU, 48940, Leioa, Spain
| | - Carlos Ibáñez
- Doñana Biological Station, CSIC, 41092, Seville, Spain
| | - Eñaut Izagirre
- University of the Basque Country UPV/EHU, 48940, Leioa, Spain.,Basque Centre for Climate Change BC3, 48940, Leioa, Spain
| | - Hugo Rebelo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade Recursos e Genéticos, Universidade do Porto, Vairão, Portugal.,CIBIO-InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017, Lisboa, Portugal
| | - Danilo Russo
- Wildlife Research Unit, Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Naples, Italy
| | - Anton Vlaschenko
- Bat Rehabilitation Center of Feldman Ecopark, Kharkiv, 62340, Ukraine
| | - Violeta Zhelyazkova
- National Museum of Natural History, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000, Sofia, Bulgaria
| | - Vida Zrnčić
- Croatian Biospeleological Society, HR-10000, Zagreb, Croatia
| | - M Thomas P Gilbert
- Centre for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, 7491, Trondheim, Norway
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14
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Uranga E, Valverde A, Salort M, Otalora M, Rodriguez P, Esnaola M, Basterretxea L, Aizpurua O, Centeno M, Moreno L, Telleria H, Landa M. Assessment of emotional discomfort of oncological patients in the first nursing visit at Donostia University Hospital. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz275.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Arrizabalaga‐Escudero A, Merckx T, García‐Baquero G, Wahlberg N, Aizpurua O, Garin I, Goiti U, Aihartza J. Trait‐based functional dietary analysis provides a better insight into the foraging ecology of bats. J Anim Ecol 2019; 88:1587-1600. [DOI: 10.1111/1365-2656.13055] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/13/2019] [Accepted: 05/31/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Aitor Arrizabalaga‐Escudero
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology University of the Basque Country UPV/EHU Leioa The Basque Country
| | - Thomas Merckx
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute UCLouvain Louvain‐La‐Neuve Belgium
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Gonzalo García‐Baquero
- Department of Plant Biology and Ecology, Faculty of Science and Technology University of the Basque Country UPV/EHU Leioa The Basque Country
| | | | - Ostaizka Aizpurua
- Section for Evolutionary Genomics University of Copenhagen Copenhagen Denmark
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology University of the Basque Country UPV/EHU Leioa The Basque Country
| | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology University of the Basque Country UPV/EHU Leioa The Basque Country
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology University of the Basque Country UPV/EHU Leioa The Basque Country
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16
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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17
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Uranga E, Valverde A, Landa M, Esnaola M, Basterretxea L, Agirre G, Aizpurua O, Barrio A, Centeno M, Delgado I, Jauregui G, Moreno L, Murguiondo M, San Francisco J, Telleria H. Standardising the psychosocial assessment of oncological patients at Donostia university hospital. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy276.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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18
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Affiliation(s)
- Ostaizka Aizpurua
- Section for Evolutionary Genomics; Natural History Museum of Denmark; University of Copenhagen; 1350 Copenhagen Denmark
| | - Antton Alberdi
- Section for Evolutionary Genomics; Natural History Museum of Denmark; University of Copenhagen; 1350 Copenhagen Denmark
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19
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Affiliation(s)
- Antton Alberdi
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen K, Denmark
| | - Ostaizka Aizpurua
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen K, Denmark
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20
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Aizpurua O, Budinski I, Georgiakakis P, Gopalakrishnan S, Ibañez C, Mata V, Rebelo H, Russo D, Szodoray-Parádi F, Zhelyazkova V, Zrncic V, Gilbert MTP, Alberdi A. Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding. Mol Ecol 2018; 27:815-825. [PMID: 29290102 DOI: 10.1111/mec.14474] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/06/2017] [Accepted: 12/08/2017] [Indexed: 01/19/2023]
Abstract
The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study, we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterize arthropod 16S and COI DNA sequences within bat faecal pellets collected across 16 Southern European localities, to first characterize the bat species' dietary niche, second measure the incidence of agricultural pests across their ranges and third assess whether geographical dietary variation responds to climatic, landscape diversity, agriculture type and vegetation productivity factors. We detected 12 arthropod orders, among which lepidopterans were predominant. We identified >200 species, 44 of which are known to cause agricultural damage. Pest species were detected at all but one sampling site and in 94% of the analysed samples. Furthermore, the dietary diversity of M. schreibersii exhibited a negative linear relation with the area of intensive agricultural fields, thus suggesting crops restrict the dietary niche of bats to prey taxa associated with agricultural production within their foraging range. Overall, our results imply that M. schreibersii might be a valuable asset for biological pest suppression in a variety of agricultural productions and highlight the dynamic interplay between wildlife and agricultural systems.
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Affiliation(s)
- Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, Serbia
| | - Panagiotis Georgiakakis
- Department of Biology School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carlos Ibañez
- Evolutionary Ecology Department, Estacion Biologica de Doñana (CSIC), Seville, Spain
| | - Vanessa Mata
- CIBIO-InBIO, Centro de Investigação em Biodiversidade Recursos e Genéticos, Universidade do Porto, Vairão, Portugal
| | - Hugo Rebelo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade Recursos e Genéticos, Universidade do Porto, Vairão, Portugal
| | - Danilo Russo
- Wildlife Research Unit, Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | | | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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21
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Affiliation(s)
- Antton Alberdi
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Trace and Environmental DNA LaboratoryDepartment of Environment and AgricultureCurtin University Perth WA Australia
- NTNU University Museum Trondheim Norway
| | - Kristine Bohmann
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- School of Biological SciencesUniversity of East Anglia Norwich Norfolk UK
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22
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Aizpurua O, Alberdi A, Aihartza J, Garin I. Fishing Technique of Long-Fingered Bats Was Developed from a Primary Reaction to Disappearing Target Stimuli. PLoS One 2016; 11:e0167164. [PMID: 27973529 PMCID: PMC5156352 DOI: 10.1371/journal.pone.0167164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/09/2016] [Indexed: 11/19/2022] Open
Abstract
Behavioral plasticity is a key feature allowing animals to broaden their dietary niche when novel food resources become available, and long-fingered bats provide an appropriate model system to study the underpinnings of behavioral plasticity, since although generally being an insectivorous species, some individuals have been reported to catch fish. Aiming to get insight into the origin of fishing behavior in long-fingered bats, we studied in the field the differences in sensorial and mechanical reactions to insect-like (stationary) and fish-like (temporary) prey stimuli between well-known piscivorous and strictly insectivorous individuals. Both piscivorous and insectivorous individuals exhibited a qualitatively similar reaction to temporary target stimuli (longer and deeper dips and terminal echolocation phase skewed towards buzz I compared to stationary stimuli). Nevertheless, the quantitative differences observed in the sensorial and mechanical features (the intensity of the shift was significantly greater in piscivorous than in insectivorous individuals) show that piscivorous individuals have honed their capture technique likely enhancing the fishing success. Thus, our results suggest that the fishing technique was developed from a primary reaction shared by all long-fingered bats. All individuals seem to be mechanically and sensorially adapted to detect and capture fish, although under appropriate environmental conditions, they would further improve their technique by experience and/or social learning.
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Affiliation(s)
- Ostaizka Aizpurua
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen K, Denmark
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z/g, Leioa, The Basque Country, Spain
| | - Antton Alberdi
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen K, Denmark
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z/g, Leioa, The Basque Country, Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z/g, Leioa, The Basque Country, Spain
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z/g, Leioa, The Basque Country, Spain
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23
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Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation? Trends Ecol Evol 2016; 31:689-699. [PMID: 27453351 DOI: 10.1016/j.tree.2016.06.008] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/18/2016] [Accepted: 06/21/2016] [Indexed: 12/14/2022]
Abstract
During times of rapid environmental change, survival of most vertebrate populations depends on their phenomic plasticity. Although differential gene-expression and post-transcriptional processes of the host genome receive focus as the main molecular mechanisms, growing evidence points to the gut microbiota as a key driver defining hosts' phenotypes. We propose that the plasticity of the gut microbiota might be an essential factor determining phenomic plasticity of vertebrates, and that it might play a pivotal role when vertebrates acclimate and adapt to fast environmental variation. We contemplate some key questions and suggest methodological approaches and experimental designs that can be used to evaluate whether gut microorganisms provide a boost of plasticity to vertebrates' phenomes, thereby increasing their acclimation and adaptation capacity.
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Affiliation(s)
- Antton Alberdi
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
| | - Ostaizka Aizpurua
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Kristine Bohmann
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7UG, UK
| | - Marie Lisandra Zepeda-Mendoza
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia; NTNU University Museum, N-7491 Trondheim, Norway.
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24
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Aizpurua O, Alberdi A, Aihartza J, Garin I. Insight on how fishing bats discern prey and adjust their mechanic and sensorial features during the attack sequence. Sci Rep 2015; 5:12392. [PMID: 26196094 PMCID: PMC4508917 DOI: 10.1038/srep12392] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/26/2015] [Indexed: 11/26/2022] Open
Abstract
Several insectivorous bats have included fish in their diet, yet little is known about the processes underlying this trophic shift. We performed three field experiments with wild fishing bats to address how they manage to discern fish from insects and adapt their hunting technique to capture fish. We show that bats react only to targets protruding above the water and discern fish from insects based on prey disappearance patterns. Stationary fish trigger short and shallow dips and a terminal echolocation pattern with an important component of the narrowband and low frequency calls. When the fish disappears during the attack process, bats regulate their attack increasing the number of broadband and high frequency calls in the last phase of the echolocation as well as by lengthening and deepening their dips. These adjustments may allow bats to obtain more valuable sensorial information and to perform dips adjusted to the level of uncertainty on the location of the submerged prey. The observed ultrafast regulation may be essential for enabling fishing to become cost-effective in bats, and demonstrates the ability of bats to rapidly modify and synchronise their sensorial and motor features as a response to last minute stimulus variations.
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Affiliation(s)
- Ostaizka Aizpurua
- Department of Zoology and Animal Cell Biology. Faculty of Science and Technology. University of The Basque Country, UPV/EHU. Sarriena z.g., E-48940 Leioa, The Basque Country
| | - Antton Alberdi
- Department of Zoology and Animal Cell Biology. Faculty of Science and Technology. University of The Basque Country, UPV/EHU. Sarriena z.g., E-48940 Leioa, The Basque Country
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology. Faculty of Science and Technology. University of The Basque Country, UPV/EHU. Sarriena z.g., E-48940 Leioa, The Basque Country
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology. Faculty of Science and Technology. University of The Basque Country, UPV/EHU. Sarriena z.g., E-48940 Leioa, The Basque Country
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Alberdi A, Aizpurua O, Aihartza J, Garin I. Unveiling the factors shaping the distribution of widely distributed alpine vertebrates, using multi-scale ecological niche modelling of the bat Plecotus macrobullaris. Front Zool 2014; 11:77. [PMID: 25389444 PMCID: PMC4226887 DOI: 10.1186/s12983-014-0077-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 10/07/2014] [Indexed: 12/28/2022] Open
Abstract
Several alpine vertebrates share a distribution pattern that extends across the South-western Palearctic but is limited to the main mountain massifs. Although they are usually regarded as cold-adapted species, the range of many alpine vertebrates also includes relatively warm areas, suggesting that factors beyond climatic conditions may be driving their distribution. In this work we first recognize the species belonging to the mentioned biogeographic group and, based on the environmental niche analysis of Plecotus macrobullaris, we identify and characterize the environmental factors constraining their ranges. Distribution overlap analysis of 504 European vertebrates was done using the Sorensen Similarity Index, and we identified four birds and one mammal that share the distribution with P. macrobullaris. We generated 135 environmental niche models including different variable combinations and regularization values for P. macrobullaris at two different scales and resolutions. After selecting the best models, we observed that topographic variables outperformed climatic predictors, and the abruptness of the landscape showed better predictive ability than elevation. The best explanatory climatic variable was mean summer temperature, which showed that P. macrobullaris is able to cope with mean temperature ranges spanning up to 16°C. The models showed that the distribution of P. macrobullaris is mainly shaped by topographic factors that provide rock-abundant and open-space habitats rather than climatic determinants, and that the species is not a cold-adapted, but rather a cold-tolerant eurithermic organism. P. macrobullaris shares its distribution pattern as well as several ecological features with five other alpine vertebrates, suggesting that the conclusions obtained from this study might be extensible to them. We concluded that rock-dwelling and open-space foraging vertebrates with broad temperature tolerance are the best candidates to show wide alpine distribution in the Western Palearctic.
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Affiliation(s)
- Antton Alberdi
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country UPV/EHU, Sarriena auzoa s/n, 48940 Leioa, The Basque Country
| | - Ostaizka Aizpurua
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country UPV/EHU, Sarriena auzoa s/n, 48940 Leioa, The Basque Country
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country UPV/EHU, Sarriena auzoa s/n, 48940 Leioa, The Basque Country
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country UPV/EHU, Sarriena auzoa s/n, 48940 Leioa, The Basque Country
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Alberdi A, Aihartza J, Aizpurua O, Salsamendi E, Brigham RM, Garin I. Living above the treeline: roosting ecology of the alpine bat Plecotus macrobullaris. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0862-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Aizpurua O, Aihartza J, Alberdi A, Baagøe HJ, Garin I. Fine-tuned echolocation and capture-flight of Myotis capaccinii when facing different-sized insect and fish prey. ACTA ACUST UNITED AC 2014; 217:3318-25. [PMID: 25013107 DOI: 10.1242/jeb.104992] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Formerly thought to be a strictly insectivorous trawling bat, recent studies have shown that Myotis capaccinii also preys on fish. To determine whether differences exist in bat flight behaviour, prey handling and echolocation characteristics when catching fish and insects of different size, we conducted a field experiment focused on the last stage of prey capture. We used synchronized video and ultrasound recordings to measure several flight and dip features as well as echolocation characteristics, focusing on terminal buzz phase I, characterized by a call rate exceeding 100 Hz, and buzz phase II, characterized by a drop in the fundamental well below 20 kHz and a repetition rate exceeding 150 Hz. When capturing insects, bats used both parts of the terminal phase to the same extent, and performed short and superficial drags on the water surface. In contrast, when preying on fish, buzz I was longer and buzz II shorter, and the bats made longer and deeper dips. These variations suggest that lengthening buzz I and shortening buzz II when fishing is beneficial, probably because buzz I gives better discrimination ability and the broader sonar beam provided by buzz II is useless when no evasive flight of the prey is expected. Additionally, bats continued emitting calls beyond the theoretical signal-overlap zone, suggesting that they might obtain information even when they have surpassed that threshold, at least initially. This study shows that M. capaccinii can regulate the temporal components of its feeding buzzes and modify prey capture technique according to the target.
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Affiliation(s)
- Ostaizka Aizpurua
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z.g., E-48940 Leioa, The Basque Country, Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z.g., E-48940 Leioa, The Basque Country, Spain
| | - Antton Alberdi
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z.g., E-48940 Leioa, The Basque Country, Spain
| | - Hans J Baagøe
- The Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of The Basque Country, UPV/EHU, Sarriena z.g., E-48940 Leioa, The Basque Country, Spain
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Alberdi A, Garin I, Aizpurua O, Aihartza J. Review on the Geographic and Elevational Distribution of the Mountain Long-Eared Bat Plecotus Macrobullaris, Completed by Utilising a Specific Mist-Netting Technique. Acta Chiropterologica 2013. [DOI: 10.3161/150811013x679071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Alberdi A, Garin I, Aizpurua O, Aihartza J. The foraging ecology of the mountain long-eared bat Plecotus macrobullaris revealed with DNA mini-barcodes. PLoS One 2012; 7:e35692. [PMID: 22545129 PMCID: PMC3335802 DOI: 10.1371/journal.pone.0035692] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/22/2012] [Indexed: 11/19/2022] Open
Abstract
Molecular analysis of diet overcomes the considerable limitations of traditional techniques for identifying prey remains in bat faeces. We collected faeces from individual Mountain Long-eared Bats Plecotus macrobullaris trapped using mist nets during the summers of 2009 and 2010 in the Pyrenees. We analysed their diet using DNA mini-barcodes to identify prey species. In addition, we inferred some basic features of the bat's foraging ecology that had not yet been addressed. P. macrobullaris fed almost exclusively on moths (97.8%). As prey we detected one dipteran genus (Tipulidae) and 29 moth taxa: 28 were identified at species level (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1 Tortricidae), and one at genus level (Rhyacia sp., Noctuidae). Known ecological information about the prey species allowed us to determine that bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean sea level), mostly in subalpine meadows, followed by other open habitats such as orophilous grasslands and alpine meadows. No forest prey species were identified in the diet. As 96.4% of identified prey species were tympanate moths and no evidence of gleaning behaviour was revealed, we suggest P. macrobullaris probably forages by aerial hawking using faint echolocation pulses to avoid detection by hearing moths. As we could identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular Operational Taxonomic Units) at species level, we conclude that DNA mini-barcodes are a very useful tool to analyse the diet of moth-specialist bats.
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Affiliation(s)
- Antton Alberdi
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Sarriena z.g., Leioa, The Basque Country
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Sarriena z.g., Leioa, The Basque Country
| | - Ostaizka Aizpurua
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Sarriena z.g., Leioa, The Basque Country
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Sarriena z.g., Leioa, The Basque Country
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Alberdi A, Aihartza J, Albero JC, Aizpurua O, López-Baucells A, Freixas L, Puig X, Flaquer C, Garin I. First records of the parti-coloured bat Vespertilio murinus (Chiroptera: Vespertilionidae) in the Pyrenees. MAMMALIA 2012. [DOI: 10.1515/mamm.2011.106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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