Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. 108, 4578–4585 (2011).
Google Scholar
Bäckhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690–703 (2015).
Google Scholar
Tanaka, M. & Nakayama, J. Development of the gut microbiota in infancy and its impact on health in later life. Allergol. Int. 66, 515–522 (2017).
Google Scholar
Xu, C., Zhu, H. & Qiu, P. Aging progression of human gut microbiota. BMC Microbiol. 19, 1–10 (2019).
Google Scholar
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).
Google Scholar
Nagpal, R. et al. Ontogenesis of the gut microbiota composition in healthy, full-term, vaginally born and breast-fed infants over the first 3 years of life: A quantitative bird’s-eye view. Front. Microbiol. 8, 1–9 (2017).
Google Scholar
Smith, S. C., Chalker, A., Dewar, M. L. & Arnould, J. P. Y. Age-related differences revealed in Australian fur seal Arctocephalus pusillus doriferus gut microbiota. FEMS Microbiol. Ecol. 86, 246–255 (2013).
Google Scholar
Janiak, M. C. et al. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques. Microbiome 9, (2021).
Toro-Valdivieso, C., Toro, F., Stubbs, S., Castro-Nallar, E. & Blacklaws, B. Patterns of the fecal microbiota in the Juan Fernández fur seal (Arctocephalus philippii). MicrobiologyOpen 10, 1–19 (2021).
Google Scholar
Medeiros, A. W. et al. Characterization of the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (Arctocephalus tropicalis). FEMS Microbiol. Ecol. 92, 1–8 (2016).
Google Scholar
Bik, E. M. et al. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat. Commun. 7, 10516 (2016).
Google Scholar
Numberger, D., Herlemann, D. P. R., Jürgens, K., Dehnhardt, G. & Schulz-Vogt, H. Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina). MicrobiologyOpen 5, 782–792 (2016).
Google Scholar
Pacheco-Sandoval, A. et al. The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences. PlosOne 14, (2019).
Nelson, T. M., Rogers, T. L., Carlini, A. R. & Brown, M. V. Diet and phylogeny shape the gut microbiota of Antarctic seals: A comparison of wild and captive animals. Environ. Microbiol. 15, 1132–1145 (2013).
Google Scholar
Glad, T. et al. Ecological characterisation of the colonic microbiota in Arctic and sub-Arctic seals. Microbiol. Ecol. 60, 320–330 (2010).
Google Scholar
Delport, T. C., Power, M. L., Harcourt, R. G., Webster, K. N. & Tetu, S. G. Colony location and captivity influence the gut microbial community composition of the Australian sea lion (Neophoca cinerea). Appl. Environ. Microbiol. 82, 3440–3349 (2016).
Google Scholar
Stoffel, M. A. et al. Early sexual dimorphism in the developing gut microbiome of northern elephant seals. Mol. Ecol. 29, 2109–2122 (2020).
Google Scholar
Tian, J., Du, J., Han, J., Song, X. & Lu, Z. Age-related differences in gut microbial community composition of captive spotted seals (Phoca largha). Mar. Mamm. Sci. 36, 1231–1240 (2020).
Google Scholar
Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011).
Google Scholar
Bigg, M. A. Harbour seal: Phoca vitulina and P. largha. In Handbook of Marine Mammals Vol. 2 (eds Ridgeway, S. H. & Harrison, R. J.) 1–27 (Academic Press, 1981).
Parracho, H., McCartney, A. L. & Gibson, G. R. Probiotics and prebiotics in infant nutrition. Proc. Nutr. Society 66, 405–411 (2007).
Google Scholar
Marques, T. M. et al. Programming infant gut microbiota: Influence of dietary and environmental factors. Curr. Opin. Biotechnol. 21, 149–156 (2010).
Google Scholar
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, 1556–1573 (2007).
Google Scholar
Mitsuoka, T. Intestinal flora and aging. Nutr. Rev. 50, 438–446 (1992).
Google Scholar
Bowen, W., Oftedal, O. & Boness, D. Mass and energy transfer during lactation in a small phocid, the harbor seal (Phoca vitulina). Physiol. Zool. 65, 844–866 (1992).
Google Scholar
Bowen, W. D., Boness, D. J. & Iverson, S. J. Diving behaviour of lactating harbour seals and their pups during maternal foraging trips. Can. J. Zool. 77, 978–988 (1999).
Google Scholar
Jørgensen, C., Lydersen, C., Brix, O. & Kovacs, K. M. Diving development in nursing harbour seal pups. J. Exp. Biol. 204, 3993–4004 (2001).
Google Scholar
Muelbert, M. M. C. & Bowen, W. D. Duration of lactation and postweaning changes in mass and body composition of harbour seal, Phoca vitulina, pups. Can. J. Zool. 71, 1405–1414 (1993).
Google Scholar
Kim, M., Cho, H. & Lee, W. Y. Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica. J. Microbiol. 58, 1018–1026 (2020).
Google Scholar
Kershaw, J. L. & Hall, A. J. Seasonal variation in harbour seal (Phoca vitulina) blubber cortisol—A novel indicator of physiological state?. Sci. Rep. 6, 1–9 (2016).
Google Scholar
Madison, A. & Kiecolt-Glaser, J. K. Stress, depression, diet, and the gut microbiota: Human–bacteria interactions at the core of psychoneuroimmunology and nutrition. Curr. Opin. Behav. Sci. 28, 105–110 (2019).
Google Scholar
Thompson, P. M., Miller, D., Cooper, R. & Hammond, P. S. Changes in the distribution and activity of female harbour seals during the breeding season: implications for their lactation strategy and mating patterns. J. Anim. Ecol. 63, 24 (1994).
Google Scholar
Raulo, A. et al. Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. J. Anim. Ecol. 87, 388–399 (2018).
Google Scholar
Song, S. J. et al. Cohabiting family members share microbiota with one another and with their dogs. Elife 2013, 1–22 (2013).
Fernández-Martin, E. M., Heckel, G., Schramm, Y. & García-Aguilar, M. C. The timing of pupping and molting of the Pacific harbor seal, Phoca vitulina richardii, at Punta Banda Estuary, Baja California, Mexico. Cienc. Mar. 42, 195–208 (2016).
Google Scholar
Oates, S. C. Survival, movements, and diet of juvenile harbor seals along central California. [Master’s thesis, San Jose State University]. (2005). https://doi.org/10.31979/etd.ra96-xhge.
Germain, L. R., Mccarthy, M. D., Koch, P. L. & Harvey, J. T. Stable carbon and nitrogen isotopes in multiple tissues of wild and captive harbor seals (Phoca vitulina) off the California coast. Mar. Mamm. Sci. 28, 542–560 (2012).
Google Scholar
Brassea-Pérez, E., Schramm, Y., Heckel, G., Chong-Robles, J. & Lago-Lestón, A. Metabarcoding analysis of the Pacific harbor seal diet in Mexico. Mar. Biol. 166, (2019).
Davis, T. A., Nguyen, H. V., Costa, D. P. & Reeds, P. J. Amino acid composition of pinniped milk. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 110, 633–639 (1995).
Google Scholar
Sauvé, C. C., van de Walle, J., Hammill, M. O., Arnould, J. P. Y. & Beauplet, G. Stomach temperature records reveal nursing behaviour and transition to solid food consumption in an unweaned mammal, the harbour seal pup (Phoca vitulina). PLoS ONE 9, (2014).
Fernández Martín, E. M. Fenología de los nacimientos, estado de salud de las crías, y estructura genética poblacional de Phoca vitulina richardii en México [Doctoral thesis, Universidad Autónoma de Baja California, Mexico]. (2018).
Gresse, R. et al. Gut microbiota dysbiosis in postweaning piglets: Understanding the keys to health. Trends Microbiol. 25, 851–873 (2017).
Google Scholar
Sommer, F. et al. The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos. Cell Rep. 14, 1655–1661 (2016).
Google Scholar
Ni, Y. et al. Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients. ISME J. 15, 3207–3220 (2021).
Google Scholar
Pacífico, C. et al. Unveiling the bovine epimural microbiota composition and putative function. Microorganisms 9, 1–23 (2021).
Google Scholar
Fenn, K. et al. Quinones are growth factors for the human gut microbiota. Microbiome 5, 161 (2017).
Google Scholar
Rodríguez, J. M. et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb. Ecol. Health Disease 26, (2015).
Thompson, P. M., Mackay, A., Tollit, D. J., Enderby, S. & Hammond, P. S. The influence of body size and sex on the characteristics of harbour seal foraging trips. Can. J. Zool. 76, 1044–1053 (1998).
Google Scholar
van Parijs, S. M., Thompson, P. M., Tollit, D. J. & Mackay, A. Distribution and activity of male harbour seals during the mating season. Anim. Behav. 54, 35–43 (1997).
Google Scholar
Bjorkland, R. H. et al. Stable isotope mixing models elucidate sex and size effects on the diet of a generalist marine predator. Mar. Ecol. Prog. Ser. 526, 213–225 (2015).
Google Scholar
Schwarz, D. et al. Large-scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern. Ecol. Evol. 8, 9889–9905 (2018).
Google Scholar
Boulva, J. Temporal variations in birth period and characteristics of newborn harbour seals. Rapports et procPs-verbaux, Reunions du Conseil International pour I’Exploration de la Mer 169, 405–408 (1975).
Bhute, S. S., Ghaskadbi, S. S. & Shouche, Y. S. Rare biosphere in human gut: A less explored component of human gut microbiota and its association with human health. In Mining of Microbial Wealth and MetaGenomics (eds Kalia, V. C. et al.) 133–142 (Springer Nature Singapore Ptd Ltd, 2017). https://doi.org/10.1007/978-981-10-5708-3.
Google Scholar
Brown, R. F. & Mate, B. R. Abundance, movements, and feeding habits of harbor seals, Phoca vitulina, at Netarts and Tillamook Bays, Oregon. Fishery Bull. 81, 291–301 (1983).
Higgins, R. Bacteria and fungi of marine mammals: A review. Can. Veterinary J. 41, 105–116 (2000).
Google Scholar
Gilbert, M. J. et al. Campylobacter blaseri sp. nov., isolated from common seals (Phoca vitulina). Int. J. Syst. Evolut. Microbiol. 68, 1787–1794 (2018).
Google Scholar
Agnese, E. D. et al. Comparative microbial community analysis of fur seals and salmon aquaculture in Tasmania. Authorea. https://doi.org/10.22541/au.160253843.32636436/v1 (2020).
Google Scholar
Rivas, A. J., Lemos, M. L. & Osorio, C. R. Photobacterium damselae subsp. damselae, a bacterium pathogenic for marine animals and humans. Front. Microbiol. 4, 1–6 (2013).
Google Scholar
Fouz, B., Toranzo, A. E., Milan, M. & Amaro, C. Evidence that water transmits the disease caused by the fish pathogen Photobacterium damselae subsp. damselae. J. Appl. Microbiol. 88, 531–535 (2000).
Google Scholar
Hundenborn, J., Thurig, S., Kommerell, M., Haag, H. & Nolte, O. Severe Wound Infection with Photobacterium damselae ssp. damselae and Vibrio harveyi, following a laceration injury in marine environment: A case report and review of the literature. Case Rep. Med. 2013, (2013).
Lubinsky-Jinich, D., Schramm, Y. & Heckel, G. The Pacific Harbor Seal’s (Phoca vitulina richardii) breeding colonies in Mexico: Abundance and distribution. Aquat. Mamm. 43, 73–81 (2017).
Google Scholar
Arias-Del Razo, A. et al. Distribution of four pinnipeds (Zalophus californianus, Arctocephalus philippii townsendi, Phoca vitulina richardii, and Mirounga angustirostris) on Islands off the west coast of the Baja California Peninsula, Mexico. Aquat. Mamm. 43, 40–51 (2017).
Google Scholar
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA. 108, 4516–4522 (2011).
Google Scholar
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).
Google Scholar
Robertson, K. M., Lauf, M. L. & Morin, P. A. Genetic sexing of pinnipeds: A real-time, single step qPCR technique. Conserv. Genet. Resour. 10, 213–218 (2018).
Google Scholar
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
Google Scholar
Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.r-project.org/ (2019). Accessed 3 June 2021.
McMurdie, P. J. & Holmes, S. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, (2013).
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-4. https://cran.r-project.org/package=vegan (2019). Accessed 3 June 2021.
Andersen, K. S., Kirkegaard, R. H., Karst, S. M. & Albertsen, M. ampvis2: An R package to analyse and visualise 16S rRNA amplicon data. bioRxiv. https://doi.org/10.1101/299537 (2018).
Google Scholar
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).
Google Scholar
Salinas, H. & Ramirez-Delgado, D. ecolTest: Community Ecology Tests. (2021).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
Google Scholar
Lozupone, C. & Knight, R. UniFrac: A new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
Google Scholar
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: An effective distance metric for microbial community comparison. ISME J. 5, 169–172 (2011).
Google Scholar
Martinez Arbizu, P. pairwiseAdonis: Pairwise multilevel comparison using adonis. R package version 0.4. (2020).
Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 685–688 (2020).
Google Scholar
Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes-A 2019 update. Nucleic Acids Res. 48, D455–D463 (2020).
Google Scholar
Source: Ecology - nature.com
