Current Role at Stanford

Microbiologist, veterinarian and data analyst in the Relman lab studying the indigenous gut microbiota of a wide range of marine and terrestrial mammals. Current research interests include characterizing microbiome assembly in neonatal mammals, host-microbiome co-evolution and patterns of microbiome diversity associated with wildlife population health.

Education & Certifications

  • PhD, Stanford School of Medicine, Microbiology & Immunology (2019)
  • Doctor of Veterinary Medicine, University of California at Davis School of Veterinary Medicine, Veterinary Medicine (2009)
  • Masters of Preventative Vet Med, University of California at Davis, Public health & zoonoses (2013)

All Publications

  • Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation. Environmental microbiology Switzer, A. D., Callahan, B. J., Costello, E. K., Bik, E. M., Fontaine, C., Gulland, F. M., Relman, D. A. 2023


    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.

    View details for DOI 10.1111/1462-2920.16444

    View details for PubMedID 37329141

  • Characterizing the oral and distal gut microbiota of the threatened southern sea otter (Enhydra lutris nereis) to enhance conservation practice. Conservation science and practice Dudek, N. K., Switzer, A. D., Costello, E. K., Murray, M. J., Tomoleoni, J. A., Staedler, M. M., Tinker, M. T., Relman, D. A. 2022; 4 (4)


    The southern sea otter (Enhydra lutris nereis) is a threatened sub-species in coastal ecosystems. To understand better the role of diet, monitor health, and enhance management of this and other marine mammal species, we characterized the oral (gingival) and distal gut (rectal and fecal) microbiota of 158 wild southern sea otters living off the coast of central California, USA, and 12 captive sea otters, some of which were included in a diet shift experiment. We found that the sea otter fecal microbiota was distinct from that of three other otter species, and that captivity does not significantly alter the community structure of the sea otter gingival or distal gut microbiota. Metagenomic analysis unexpectedly revealed that the majority of sea otter fecal DNA is derived from prey, rather than from indigenous bacteria or host cells as with most other mammals. We speculate that a reduced bacterial biomass in the sea otter gut reflects rapid gut transit time and a particular strategy for foraging and energy harvest. This study establishes a reference for the healthy sea otter microbiota, highlights how a marine lifestyle may shape the mammalian microbiota, and may inform future health assessments and conservation management of sea otter populations.

    View details for DOI 10.1111/csp2.12640

    View details for PubMedID 35382031

    View details for PubMedCentralID PMC8979051

  • Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder. Frontiers in microbiology Roth, T. L., Switzer, A., Watanabe-Chailland, M., Bik, E. M., Relman, D. A., Romick-Rosendale, L. E., Ollberding, N. J. 2019; 10: 2291


    Iron overload disorder (IOD) affects many wildlife species cared for ex situ. Two of the four rhinoceros species in human care, Sumatran rhinoceros (Dicerorhinus sumatrensis) and black rhinoceros (Diceros bicornis), are susceptible, whereas the other two, white rhinoceros (Ceratotherium simum) and greater one-horned (GOH) rhinoceros (Rhinoceros unicornis), are relatively resistant to IOD. Complex interrelationships exist between mammalian hosts, their indigenous gut microbiota, metabolome, physical condition, and iron availability. The goal of this study was to gain insight into these relationships within the family Rhinocerotidae. Specific objectives were to (1) characterize the gut microbiome and metabolome of four rhinoceros species; (2) compare the microbiome and metabolome of IOD-susceptible and IOD-resistant rhinoceros species; and (3) identify variation in the microbiome and metabolome associated with compromised health or disease in IOD-susceptible rhinoceroses. Fecal samples were collected from 31 rhinoceroses (Sumatran rhinoceros, n = 3; black rhinoceros, n = 6; GOH rhinoceros, n = 9; white rhinoceros, n = 13) located at five facilities, and matched fecal aliquots were processed for microbiome and metabolome analyses using 16S rRNA gene sequencing and nuclear magnetic resonance spectroscopy, respectively. Despite the phylogenetic disparity and dissimilar zoo diets of the hosts, the structure of the fecal microbiota of the two IOD-susceptible rhinoceros species were more closely related to each other than to those of the two IOD-resistant species (Bray-Curtis dissimilarity; IOD-susceptible vs. IOD-resistant p-value < 0.001). In addition, IOD-susceptible rhinoceroses exhibited less microbial diversity than their IOD-resistant relatives (Shannon diversity; p-value < 0.001) which could have health implications. Of note, the black rhinoceros was distinct among the four rhinoceros species with the most divergent fecal metabolome; interestingly, it contained higher concentrations of short chain fatty acids. Neither age nor sex were associated with differences in microbial community composition (p = 0.253 and 0.488, respectively) or fecal metabolomic profile (p = 0.634 and 0.332, respectively). Differences in the distal gut microbiomes between IOD-resistant and IOD-susceptible rhinoceroses support hypotheses that gut microbes play a role in host iron acquisition, and further studies and experiments to test these hypotheses are warranted.

    View details for DOI 10.3389/fmicb.2019.02291

    View details for PubMedID 31649637

  • Namibian farmland cheetahs (Acinonyx jubatus) demonstrate seronegativity for antibodies against Bacillus anthracis AFRICAN JOURNAL OF WILDLIFE RESEARCH Switzer, A., Munson, L., Beesley, C., Wilkins, P., Blackburn, J. K., Marker, L. 2016; 46 (2): 139-143
  • Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nature communications Bik, E. M., Costello, E. K., Switzer, A. D., Callahan, B. J., Holmes, S. P., Wells, R. S., Carlin, K. P., Jensen, E. D., Venn-Watson, S., Relman, D. A. 2016; 7: 10516-?


    Marine mammals play crucial ecological roles in the oceans, but little is known about their microbiotas. Here we study the bacterial communities in 337 samples from 5 body sites in 48 healthy dolphins and 18 healthy sea lions, as well as those of adjacent seawater and other hosts. The bacterial taxonomic compositions are distinct from those of other mammals, dietary fish and seawater, are highly diverse and vary according to body site and host species. Dolphins harbour 30 bacterial phyla, with 25 of them in the mouth, several abundant but poorly characterized Tenericutes species in gastric fluid and a surprisingly paucity of Bacteroidetes in distal gut. About 70% of near-full length bacterial 16S ribosomal RNA sequences from dolphins are unique. Host habitat, diet and phylogeny all contribute to variation in marine mammal distal gut microbiota composition. Our findings help elucidate the factors structuring marine mammal microbiotas and may enhance monitoring of marine mammal health.

    View details for DOI 10.1038/ncomms10516

    View details for PubMedID 26839246

    View details for PubMedCentralID PMC4742810

  • Bartonella and Toxoplasma Infections in Stray Cats from Iraq AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Switzer, A. D., McMillan-Cole, A. C., Kasten, R. W., Stuckey, M. J., Kass, P. H., Chomel, B. B. 2013; 89 (6): 1219-1224


    Because of overpopulation, stray/feral cats were captured on military bases in Iraq as part of the US Army Zoonotic Disease Surveillance Program. Blood samples were collected from 207 cats, mainly in Baghdad but also in North and West Iraq, to determine the prevalence of Bartonella and Toxoplasma infections. Nine (4.3%) cats, all from Baghdad, were bacteremic with B. henselae type I. Seroprevalence was 30.4% for T. gondii, 15% for B. henselae, and 12.6% for B. clarridgeiae. Differences in Bartonella prevalence by location were statistically significant, because most of the seropositive cats were from Baghdad. There was no association between T. gondii seropositivity and either of the two Bartonella species surveyed. This report is the first report on the prevalence of Bartonella and T. gondii among stray cats in Iraq, which allows for better evaluation of the zoonotic risk potential to the Iraqi people and deployed military personnel by feral cat colonies.

    View details for DOI 10.4269/ajtmh.13-0353

    View details for Web of Science ID 000328726100028

    View details for PubMedID 24062480

    View details for PubMedCentralID PMC3854905

  • Infection of pregnant mice with Listeria monocytogenes induces fetal bradycardia PEDIATRIC RESEARCH Hardy, J., Kirkendoll, B., Zhao, H., Pisani, L., Luong, R., Switzer, A., McConnell, M. V., Contag, C. H. 2012; 71 (5): 539-545


    Listeriosis is one of the most lethal bacterial diseases for fetuses and infants. However, pregnant women who get infected with Listeria may experience only mild symptoms, making the diagnosis difficult, even when the fetus is fatally infected.To reveal features of this infection, we conducted a multimodality imaging study of Listeria-induced miscarriage, using a pregnant mouse model. In this model, fetal morbidity and mortality can be observed in utero, noninvasively, and the timing and extent of infection can be carefully controlled. By employing in vivo bioluminescence imaging (BLI), perinatal infections were localized over time such that a correlation of infection to outcome could be determined without the need to kill the animal subject. The morbidity and viability of fetuses were assessed with ultrasound, and fetal morphology was imaged using magnetic resonance imaging (MRI).The ultrasound revealed sustained fetal bradycardia, the slowing of the fetal heartbeat, in infected fetuses, with an association between slowed fetal heart rate and strong bioluminescent signal.Uninfected fetuses showing no bioluminescent signal in the same uterine horn exhibited normal heartbeats. Thus, fetal bradycardia during infection was localized to the infected fetus and was not systemic or disseminated.

    View details for DOI 10.1038/pr.2012.2

    View details for PubMedID 22314663