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Switzer AD, Callahan BJ, Costello EK, Bik EM, Fontaine C, Gulland FM, Relman DA. Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation. Environ Microbiol 2023; 25:2182-2202. [PMID: 37329141 PMCID: PMC11180496 DOI: 10.1111/1462-2920.16444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 05/22/2023] [Indexed: 06/18/2023]
Abstract
Microbial community assembly remains largely unexplored in marine mammals, despite its potential importance for conservation and management. Here, neonatal microbiota assembly was studied in harbour seals (Phoca vitulina richardii) at a rehabilitation facility soon after maternal separation, through weaning, to the time of release back to their native environment. We found that the gingival and rectal communities of rehabilitated harbour seals were distinct from the microbiotas of formula and pool water, and became increasingly diverse and dissimilar over time, ultimately resembling the gingival and rectal communities of local wild harbour seals. Harbour seal microbiota assembly was compared to that of human infants, revealing the rapid emergence of host specificity and evidence of phylosymbiosis even though these harbour seals had been raised by humans. Early life prophylactic antibiotics were associated with changes in the composition of the harbour seal gingival and rectal communities and surprisingly, with transient increases in alpha diversity, perhaps because of microbiota sharing during close cohabitation with other harbour seals. Antibiotic-associated effects dissipated over time. These results suggest that while early life maternal contact may provide seeding for microbial assembly, co-housing of conspecifics during rehabilitation may help neonatal mammals achieve a healthy host-specific microbiota with features of resilience.
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Affiliation(s)
- Alexandra D. Switzer
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Benjamin J. Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Department of Statistics, Stanford University, Stanford, CA, United States
| | - Elizabeth K. Costello
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | | | | | - Frances M.D. Gulland
- The Marine Mammal Center, Sausalito, CA, United States
- Wildlife Health Center, School of Veterinary Medicine, University of California at Davis, Davis, CA, United States
| | - David A. Relman
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
- Infectious Diseases Section, VA Palo Alto Health Care System, Palo Alto, CA, United States
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Pereida-Aguilar JC, Barragán-Vargas C, Domínguez-Sánchez C, Álvarez-Martínez RC, Acevedo-Whitehouse K. Bacterial dysbiosis and epithelial status of the California sea lion (Zalophus californianus) in the Gulf of California. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105474. [PMID: 37356747 DOI: 10.1016/j.meegid.2023.105474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Despite the high incidence of urogenital carcinoma (UGC) in California sea lions stranded along California, no UGC has been reported in other areas of their distribution; however, cell morphologies typical of premalignant states have been found. Risk factors for UGC include high of organochlorines and infection with a gammaherpesvirus, OtHV-1, but the importance of the bacteriome for epithelial status remains unknown. We characterized the genital bacteriome of adult female California sea lions along their distribution in the Gulf of California and examined whether the diversity and abundance of the bacteriome varied spatially, whether there were detectable differences in the bacteriome between healthy and altered epithelia, and whether the bacteriome was different in California sea lions infected with OtHV-1 or papillomavirus. We detected 2270 ASVs in the genital samples, of which 35 met the criteria for inclusion in the core bacteriome. Fusobacteriia and Clostridia were present in all samples, at high abundances, and Actinobacteria, Alphaproteobacteria, and Campylobacteria were also well-represented. Alpha diversity and abundance of the California sea lion genital bacteriome varied geographically. The abundance of bacterial ASVs varied depending on the genital epithelial status and inflammation, with differences driven by classes Fusobacteriia, Clostridia, Campylobacteria and Alphaproteobacteria. Alpha diversity and abundance were lowest in samples in which OtHV-1 was detected, and highest those with papillomavirus. Our study is the first investigation of how the bacteriome is related to epithelial status in a wild marine species prone to developing cancer.
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Affiliation(s)
- Juan Carlos Pereida-Aguilar
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Cecilia Barragán-Vargas
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Carlos Domínguez-Sánchez
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Roberto Carlos Álvarez-Martínez
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico
| | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Santiago de Queretaro 76146, Mexico.
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Mocé ML, Esteve IC, Pérez-Fuentes S, Gómez EA, Mocé E. Microbiota in Goat Buck Ejaculates Differs Between Breeding and Non-breeding Seasons. Front Vet Sci 2022; 9:867671. [PMID: 35647092 PMCID: PMC9136232 DOI: 10.3389/fvets.2022.867671] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/21/2022] [Indexed: 01/04/2023] Open
Abstract
Changes in semen microbiota are associated with alterations to sperm quality and fertility. However, the microbiota from most livestock species has not yet been studied. Goats are seasonal breeders, but semen microbiota has never been described in this species, and it is unknown how seasonality affects it. Our study objective is 2-fold: to describe the microbiota in goat buck ejaculates and to determine if it differs between breeding and non-breeding seasons. Semen from six males of the Murciano-Granadina breed was collected during both seasons. Two replicates were performed per male and season on different days. The microbiota was characterized by genomic sequencing technology. Sperm quality was also evaluated. Repetition was not significant for the studied variables. Sperm velocities were higher for the breeding than for the non-breeding season. The ejaculates from both seasons also differed in the proportion of apoptotic spermatozoa. The five dominant phyla were Firmicutes, Proteobacteria, Fusobacteria, Actinobacteria, and Bacteroidetes during the breeding season and Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria during the non-breeding season. The dominant genus during both seasons was Ureaplasma. Differences in microbial community structure (the beta diversity) were found. A decrease in the relative abundance of the genus Faecalibacterium and an increase in the genera Sphingomonas and Halomonas were observed in the ejaculates collected during the breeding season. Sphingomonas and Faecalibacterium abundance favorably and unfavorably correlated with sperm quality, respectively. In conclusion, the semen microbiota from goat bucks varies between breeding and non-breeding seasons, and the microbiota remains stable for 7 days within a season. In addition, the genera Sphingomonas and Faecalibacterium could be possible biomarkers of semen quality in goat bucks. These results contribute to an in-depth understanding of the effects of reproductive seasonality on goat buck ejaculates.
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Affiliation(s)
- María Lorena Mocé
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology (PASAPTA), Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
| | - Inés Carolina Esteve
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Sara Pérez-Fuentes
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Ernesto A. Gómez
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Eva Mocé
- Unidad Asociada UCH-CEU – IVIA, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- *Correspondence: Eva Mocé
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Rhodes LD, Emmons CK, Wisswaesser G, Wells AH, Hanson MB. Bacterial microbiomes from mucus and breath of southern resident killer whales ( Orcinus orca). CONSERVATION PHYSIOLOGY 2022; 10:coac014. [PMID: 35492424 PMCID: PMC9041426 DOI: 10.1093/conphys/coac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/07/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were unique to breath and mucus, including higher abundances of Burkholderiaceae, Moraxellaceae and Chitinophagaceae. Although there were multiple bacterial genera in breath or mucus that include pathogenic species (e.g. Campylobacter, Hemophilus, Treponema), the presence of these bacteria is not necessarily evidence of disease or infection. Future emphasis on genotyping mucus samples to the individual animal will allow further assessment in the context of that animal's history, including body condition index and prior contaminants burden. This study is the first to examine expelled mucus from cetaceans for microbiomes and demonstrates the value of analysing these types of non-invasive samples.
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Affiliation(s)
- Linda D Rhodes
- Corresponding author: Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA.
| | - Candice K Emmons
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - GabrielS Wisswaesser
- Lynker Technologies, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - Abigail H Wells
- Lynker Technologies, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
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Glaeser SP, Silva LMR, Prieto R, Silva MA, Franco A, Kämpfer P, Hermosilla C, Taubert A, Eisenberg T. A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales. MICROBIAL ECOLOGY 2022; 83:18-33. [PMID: 33745062 PMCID: PMC8881428 DOI: 10.1007/s00248-021-01729-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/03/2021] [Indexed: 05/08/2023]
Abstract
Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.
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Affiliation(s)
- Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Liliana M R Silva
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Rui Prieto
- Institute of Marine Research (IMAR) and Okeanos R&D Centre, University of the Azores, Horta, Portugal
- MARE-Marine and Environmental Sciences Centre, Lisbon, Portugal
| | - Mónica A Silva
- Institute of Marine Research (IMAR) and Okeanos R&D Centre, University of the Azores, Horta, Portugal
| | - Angel Franco
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Carlos Hermosilla
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Anja Taubert
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), Giessen, Germany
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